partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
train | find_consensus | find consensus base based on nucleotide
frequencies | ctbBio/genome_variation.py | def find_consensus(bases):
"""
find consensus base based on nucleotide
frequencies
"""
nucs = ['A', 'T', 'G', 'C', 'N']
total = sum([bases[nuc] for nuc in nucs if nuc in bases])
# save most common base as consensus (random nuc if there is a tie)
try:
top = max([bases[nuc] for nuc... | def find_consensus(bases):
"""
find consensus base based on nucleotide
frequencies
"""
nucs = ['A', 'T', 'G', 'C', 'N']
total = sum([bases[nuc] for nuc in nucs if nuc in bases])
# save most common base as consensus (random nuc if there is a tie)
try:
top = max([bases[nuc] for nuc... | [
"find",
"consensus",
"base",
"based",
"on",
"nucleotide",
"frequencies"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_variation.py#L371-L402 | [
"def",
"find_consensus",
"(",
"bases",
")",
":",
"nucs",
"=",
"[",
"'A'",
",",
"'T'",
",",
"'G'",
",",
"'C'",
",",
"'N'",
"]",
"total",
"=",
"sum",
"(",
"[",
"bases",
"[",
"nuc",
"]",
"for",
"nuc",
"in",
"nucs",
"if",
"nuc",
"in",
"bases",
"]",... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | calc_frequencies | print bp frequencies to table
genomes = {} # genomes[genome][contig][sample] = {'bp_stats':{}} | ctbBio/genome_variation.py | def calc_frequencies(genomes, bp_table, min_cov, min_per):
"""
print bp frequencies to table
genomes = {} # genomes[genome][contig][sample] = {'bp_stats':{}}
"""
nucs = ['A', 'T', 'G', 'C', 'N']
if bp_table is not False:
bp_table = open(bp_table, 'w')
header = ['#genome', 'contig... | def calc_frequencies(genomes, bp_table, min_cov, min_per):
"""
print bp frequencies to table
genomes = {} # genomes[genome][contig][sample] = {'bp_stats':{}}
"""
nucs = ['A', 'T', 'G', 'C', 'N']
if bp_table is not False:
bp_table = open(bp_table, 'w')
header = ['#genome', 'contig... | [
"print",
"bp",
"frequencies",
"to",
"table",
"genomes",
"=",
"{}",
"#",
"genomes",
"[",
"genome",
"]",
"[",
"contig",
"]",
"[",
"sample",
"]",
"=",
"{",
"bp_stats",
":",
"{}",
"}"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_variation.py#L404-L449 | [
"def",
"calc_frequencies",
"(",
"genomes",
",",
"bp_table",
",",
"min_cov",
",",
"min_per",
")",
":",
"nucs",
"=",
"[",
"'A'",
",",
"'T'",
",",
"'G'",
",",
"'C'",
",",
"'N'",
"]",
"if",
"bp_table",
"is",
"not",
"False",
":",
"bp_table",
"=",
"open",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | print_consensus | print consensensus sequences for each genome and sample | ctbBio/genome_variation.py | def print_consensus(genomes):
"""
print consensensus sequences for each genome and sample
"""
# generate consensus sequences
cons = {} # cons[genome][sample][contig] = consensus
for genome, contigs in list(genomes.items()):
cons[genome] = {}
for contig, samples in list(contigs.it... | def print_consensus(genomes):
"""
print consensensus sequences for each genome and sample
"""
# generate consensus sequences
cons = {} # cons[genome][sample][contig] = consensus
for genome, contigs in list(genomes.items()):
cons[genome] = {}
for contig, samples in list(contigs.it... | [
"print",
"consensensus",
"sequences",
"for",
"each",
"genome",
"and",
"sample"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_variation.py#L451-L478 | [
"def",
"print_consensus",
"(",
"genomes",
")",
":",
"# generate consensus sequences",
"cons",
"=",
"{",
"}",
"# cons[genome][sample][contig] = consensus",
"for",
"genome",
",",
"contigs",
"in",
"list",
"(",
"genomes",
".",
"items",
"(",
")",
")",
":",
"cons",
"[... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | print_stats | print substitution rate data to table
genomes[genome][contig][sample] = \
{'bp_stats':{}, 'sub_rates'[locus] = {ref PnPs, consensus PnPs}} | ctbBio/genome_variation.py | def print_stats(genomes):
"""
print substitution rate data to table
genomes[genome][contig][sample] = \
{'bp_stats':{}, 'sub_rates'[locus] = {ref PnPs, consensus PnPs}}
"""
header = ['#genome', 'contig', 'locus', 'position', 'strand', 'length', \
'sample', 'coverage', \
... | def print_stats(genomes):
"""
print substitution rate data to table
genomes[genome][contig][sample] = \
{'bp_stats':{}, 'sub_rates'[locus] = {ref PnPs, consensus PnPs}}
"""
header = ['#genome', 'contig', 'locus', 'position', 'strand', 'length', \
'sample', 'coverage', \
... | [
"print",
"substitution",
"rate",
"data",
"to",
"table",
"genomes",
"[",
"genome",
"]",
"[",
"contig",
"]",
"[",
"sample",
"]",
"=",
"\\",
"{",
"bp_stats",
":",
"{}",
"sub_rates",
"[",
"locus",
"]",
"=",
"{",
"ref",
"PnPs",
"consensus",
"PnPs",
"}}"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_variation.py#L480-L504 | [
"def",
"print_stats",
"(",
"genomes",
")",
":",
"header",
"=",
"[",
"'#genome'",
",",
"'contig'",
",",
"'locus'",
",",
"'position'",
",",
"'strand'",
",",
"'length'",
",",
"'sample'",
",",
"'coverage'",
",",
"'ref. Pn/Ps'",
",",
"'ref SNP density'",
",",
"'c... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | variation | quantify genomic variation from mapping
genomes[genome][contig][sample] = \
{'bp_stats':[], 'sub_rates'[locus] = {ref PnPs, consensus PnPs, ...}} | ctbBio/genome_variation.py | def variation(fastas, sams, s2b, annots, qual, min_cov, min_per, no_sub, bp_table, print_con):
"""
quantify genomic variation from mapping
genomes[genome][contig][sample] = \
{'bp_stats':[], 'sub_rates'[locus] = {ref PnPs, consensus PnPs, ...}}
"""
genomes = {}
# save base-pair data... | def variation(fastas, sams, s2b, annots, qual, min_cov, min_per, no_sub, bp_table, print_con):
"""
quantify genomic variation from mapping
genomes[genome][contig][sample] = \
{'bp_stats':[], 'sub_rates'[locus] = {ref PnPs, consensus PnPs, ...}}
"""
genomes = {}
# save base-pair data... | [
"quantify",
"genomic",
"variation",
"from",
"mapping",
"genomes",
"[",
"genome",
"]",
"[",
"contig",
"]",
"[",
"sample",
"]",
"=",
"\\",
"{",
"bp_stats",
":",
"[]",
"sub_rates",
"[",
"locus",
"]",
"=",
"{",
"ref",
"PnPs",
"consensus",
"PnPs",
"...",
"}... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_variation.py#L506-L544 | [
"def",
"variation",
"(",
"fastas",
",",
"sams",
",",
"s2b",
",",
"annots",
",",
"qual",
",",
"min_cov",
",",
"min_per",
",",
"no_sub",
",",
"bp_table",
",",
"print_con",
")",
":",
"genomes",
"=",
"{",
"}",
"# save base-pair data structures for each genome-samp... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | calc_custom | custom = {(reads mapped to scaffold)/(total reads for sample)}/(length of scaffold) | ctbBio/genome_abundance.py | def calc_custom(custom, genome, scaffold, sequence, scaffold_coverage, total_bases):
"""
custom = {(reads mapped to scaffold)/(total reads for sample)}/(length of scaffold)
"""
index = 0
if scaffold in scaffold_coverage: # what if the scaffold does not have bases mapped back to it? (this *should* not happen)
if ... | def calc_custom(custom, genome, scaffold, sequence, scaffold_coverage, total_bases):
"""
custom = {(reads mapped to scaffold)/(total reads for sample)}/(length of scaffold)
"""
index = 0
if scaffold in scaffold_coverage: # what if the scaffold does not have bases mapped back to it? (this *should* not happen)
if ... | [
"custom",
"=",
"{",
"(",
"reads",
"mapped",
"to",
"scaffold",
")",
"/",
"(",
"total",
"reads",
"for",
"sample",
")",
"}",
"/",
"(",
"length",
"of",
"scaffold",
")"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_abundance.py#L13-L27 | [
"def",
"calc_custom",
"(",
"custom",
",",
"genome",
",",
"scaffold",
",",
"sequence",
",",
"scaffold_coverage",
",",
"total_bases",
")",
":",
"index",
"=",
"0",
"if",
"scaffold",
"in",
"scaffold_coverage",
":",
"# what if the scaffold does not have bases mapped back t... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | absolute_abundance | absolute abundance = (number of bases mapped to genome / total number of bases in sample) * 100 | ctbBio/genome_abundance.py | def absolute_abundance(coverage, total_bases):
"""
absolute abundance = (number of bases mapped to genome / total number of bases in sample) * 100
"""
absolute = {}
for genome in coverage:
absolute[genome] = []
index = 0
for calc in coverage[genome]:
bases = calc[0]
total = total_bases[index]
absolu... | def absolute_abundance(coverage, total_bases):
"""
absolute abundance = (number of bases mapped to genome / total number of bases in sample) * 100
"""
absolute = {}
for genome in coverage:
absolute[genome] = []
index = 0
for calc in coverage[genome]:
bases = calc[0]
total = total_bases[index]
absolu... | [
"absolute",
"abundance",
"=",
"(",
"number",
"of",
"bases",
"mapped",
"to",
"genome",
"/",
"total",
"number",
"of",
"bases",
"in",
"sample",
")",
"*",
"100"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_abundance.py#L45-L65 | [
"def",
"absolute_abundance",
"(",
"coverage",
",",
"total_bases",
")",
":",
"absolute",
"=",
"{",
"}",
"for",
"genome",
"in",
"coverage",
":",
"absolute",
"[",
"genome",
"]",
"=",
"[",
"]",
"index",
"=",
"0",
"for",
"calc",
"in",
"coverage",
"[",
"geno... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | relative_abundance | cov = number of bases / length of genome
relative abundance = [(cov) / sum(cov for all genomes)] * 100 | ctbBio/genome_abundance.py | def relative_abundance(coverage):
"""
cov = number of bases / length of genome
relative abundance = [(cov) / sum(cov for all genomes)] * 100
"""
relative = {}
sums = []
for genome in coverage:
for cov in coverage[genome]:
sums.append(0)
break
for genome in coverage:
index = 0
for cov in coverage[geno... | def relative_abundance(coverage):
"""
cov = number of bases / length of genome
relative abundance = [(cov) / sum(cov for all genomes)] * 100
"""
relative = {}
sums = []
for genome in coverage:
for cov in coverage[genome]:
sums.append(0)
break
for genome in coverage:
index = 0
for cov in coverage[geno... | [
"cov",
"=",
"number",
"of",
"bases",
"/",
"length",
"of",
"genome",
"relative",
"abundance",
"=",
"[",
"(",
"cov",
")",
"/",
"sum",
"(",
"cov",
"for",
"all",
"genomes",
")",
"]",
"*",
"100"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_abundance.py#L67-L92 | [
"def",
"relative_abundance",
"(",
"coverage",
")",
":",
"relative",
"=",
"{",
"}",
"sums",
"=",
"[",
"]",
"for",
"genome",
"in",
"coverage",
":",
"for",
"cov",
"in",
"coverage",
"[",
"genome",
"]",
":",
"sums",
".",
"append",
"(",
"0",
")",
"break",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | genome_coverage | coverage = (number of bases / length of genome) * 100 | ctbBio/genome_abundance.py | def genome_coverage(genomes, scaffold_coverage, total_bases):
"""
coverage = (number of bases / length of genome) * 100
"""
coverage = {}
custom = {}
std = {}
for genome in genomes:
for sequence in parse_fasta(genome):
scaffold = sequence[0].split('>')[1].split()[0]
coverage, std = sum_coverage(coverage,... | def genome_coverage(genomes, scaffold_coverage, total_bases):
"""
coverage = (number of bases / length of genome) * 100
"""
coverage = {}
custom = {}
std = {}
for genome in genomes:
for sequence in parse_fasta(genome):
scaffold = sequence[0].split('>')[1].split()[0]
coverage, std = sum_coverage(coverage,... | [
"coverage",
"=",
"(",
"number",
"of",
"bases",
"/",
"length",
"of",
"genome",
")",
"*",
"100"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_abundance.py#L116-L146 | [
"def",
"genome_coverage",
"(",
"genomes",
",",
"scaffold_coverage",
",",
"total_bases",
")",
":",
"coverage",
"=",
"{",
"}",
"custom",
"=",
"{",
"}",
"std",
"=",
"{",
"}",
"for",
"genome",
"in",
"genomes",
":",
"for",
"sequence",
"in",
"parse_fasta",
"("... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | parse_cov | calculate genome coverage from scaffold coverage table | ctbBio/genome_coverage.py | def parse_cov(cov_table, scaffold2genome):
"""
calculate genome coverage from scaffold coverage table
"""
size = {} # size[genome] = genome size
mapped = {} # mapped[genome][sample] = mapped bases
# parse coverage files
for line in open(cov_table):
line = line.strip().split('\t')
... | def parse_cov(cov_table, scaffold2genome):
"""
calculate genome coverage from scaffold coverage table
"""
size = {} # size[genome] = genome size
mapped = {} # mapped[genome][sample] = mapped bases
# parse coverage files
for line in open(cov_table):
line = line.strip().split('\t')
... | [
"calculate",
"genome",
"coverage",
"from",
"scaffold",
"coverage",
"table"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_coverage.py#L13-L50 | [
"def",
"parse_cov",
"(",
"cov_table",
",",
"scaffold2genome",
")",
":",
"size",
"=",
"{",
"}",
"# size[genome] = genome size",
"mapped",
"=",
"{",
"}",
"# mapped[genome][sample] = mapped bases",
"# parse coverage files",
"for",
"line",
"in",
"open",
"(",
"cov_table",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | genome_coverage | calculate genome coverage from scaffold coverage | ctbBio/genome_coverage.py | def genome_coverage(covs, s2b):
"""
calculate genome coverage from scaffold coverage
"""
COV = []
for cov in covs:
COV.append(parse_cov(cov, s2b))
return pd.concat(COV) | def genome_coverage(covs, s2b):
"""
calculate genome coverage from scaffold coverage
"""
COV = []
for cov in covs:
COV.append(parse_cov(cov, s2b))
return pd.concat(COV) | [
"calculate",
"genome",
"coverage",
"from",
"scaffold",
"coverage"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_coverage.py#L52-L59 | [
"def",
"genome_coverage",
"(",
"covs",
",",
"s2b",
")",
":",
"COV",
"=",
"[",
"]",
"for",
"cov",
"in",
"covs",
":",
"COV",
".",
"append",
"(",
"parse_cov",
"(",
"cov",
",",
"s2b",
")",
")",
"return",
"pd",
".",
"concat",
"(",
"COV",
")"
] | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | parse_s2bs | convert s2b files to dictionary | ctbBio/genome_coverage.py | def parse_s2bs(s2bs):
"""
convert s2b files to dictionary
"""
s2b = {}
for s in s2bs:
for line in open(s):
line = line.strip().split('\t')
s, b = line[0], line[1]
s2b[s] = b
return s2b | def parse_s2bs(s2bs):
"""
convert s2b files to dictionary
"""
s2b = {}
for s in s2bs:
for line in open(s):
line = line.strip().split('\t')
s, b = line[0], line[1]
s2b[s] = b
return s2b | [
"convert",
"s2b",
"files",
"to",
"dictionary"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_coverage.py#L61-L71 | [
"def",
"parse_s2bs",
"(",
"s2bs",
")",
":",
"s2b",
"=",
"{",
"}",
"for",
"s",
"in",
"s2bs",
":",
"for",
"line",
"in",
"open",
"(",
"s",
")",
":",
"line",
"=",
"line",
".",
"strip",
"(",
")",
".",
"split",
"(",
"'\\t'",
")",
"s",
",",
"b",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | fa2s2b | convert fastas to s2b dictionary | ctbBio/genome_coverage.py | def fa2s2b(fastas):
"""
convert fastas to s2b dictionary
"""
s2b = {}
for fa in fastas:
for seq in parse_fasta(fa):
s = seq[0].split('>', 1)[1].split()[0]
s2b[s] = fa.rsplit('/', 1)[-1].rsplit('.', 1)[0]
return s2b | def fa2s2b(fastas):
"""
convert fastas to s2b dictionary
"""
s2b = {}
for fa in fastas:
for seq in parse_fasta(fa):
s = seq[0].split('>', 1)[1].split()[0]
s2b[s] = fa.rsplit('/', 1)[-1].rsplit('.', 1)[0]
return s2b | [
"convert",
"fastas",
"to",
"s2b",
"dictionary"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/genome_coverage.py#L73-L82 | [
"def",
"fa2s2b",
"(",
"fastas",
")",
":",
"s2b",
"=",
"{",
"}",
"for",
"fa",
"in",
"fastas",
":",
"for",
"seq",
"in",
"parse_fasta",
"(",
"fa",
")",
":",
"s",
"=",
"seq",
"[",
"0",
"]",
".",
"split",
"(",
"'>'",
",",
"1",
")",
"[",
"1",
"]"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | eth_addr | eth_addr
:param f: eth frame | network_pipeline/parse_network_data.py | def eth_addr(f):
"""eth_addr
:param f: eth frame
"""
data = "%.2x:%.2x:%.2x:%.2x:%.2x:%.2x" % (f[0],
f[1],
f[2],
f[3],
... | def eth_addr(f):
"""eth_addr
:param f: eth frame
"""
data = "%.2x:%.2x:%.2x:%.2x:%.2x:%.2x" % (f[0],
f[1],
f[2],
f[3],
... | [
"eth_addr"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/parse_network_data.py#L41-L52 | [
"def",
"eth_addr",
"(",
"f",
")",
":",
"data",
"=",
"\"%.2x:%.2x:%.2x:%.2x:%.2x:%.2x\"",
"%",
"(",
"f",
"[",
"0",
"]",
",",
"f",
"[",
"1",
"]",
",",
"f",
"[",
"2",
"]",
",",
"f",
"[",
"3",
"]",
",",
"f",
"[",
"4",
"]",
",",
"f",
"[",
"5",
... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | parse_network_data | build_node
:param data_packet: raw recvfrom data
:param filter_keys: list of strings to filter
and remove baby-birding
packets to yourself
:param record_tcp: want to record TCP frames?
:param record_udp: want to record UDP frames?
:param record_arp: w... | network_pipeline/parse_network_data.py | def parse_network_data(data_packet=None,
include_filter_key=None,
filter_keys=[],
record_tcp=True,
record_udp=True,
record_arp=True,
record_icmp=True):
"""build_node
:param ... | def parse_network_data(data_packet=None,
include_filter_key=None,
filter_keys=[],
record_tcp=True,
record_udp=True,
record_arp=True,
record_icmp=True):
"""build_node
:param ... | [
"build_node"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/parse_network_data.py#L75-L552 | [
"def",
"parse_network_data",
"(",
"data_packet",
"=",
"None",
",",
"include_filter_key",
"=",
"None",
",",
"filter_keys",
"=",
"[",
"]",
",",
"record_tcp",
"=",
"True",
",",
"record_udp",
"=",
"True",
",",
"record_arp",
"=",
"True",
",",
"record_icmp",
"=",
... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | filter_ambiguity | Filters out sequences with too much ambiguity as defined by the method
parameters.
:type records: list
:param records: A list of sequences
:type repeats: int
:param repeats: Defines the number of repeated N that trigger truncating a
sequence.
:type percent: float
:param ... | bin/filter_ambiguity.py | def filter_ambiguity(records, percent=0.5): # , repeats=6)
"""
Filters out sequences with too much ambiguity as defined by the method
parameters.
:type records: list
:param records: A list of sequences
:type repeats: int
:param repeats: Defines the number of repeated N that trigger truncat... | def filter_ambiguity(records, percent=0.5): # , repeats=6)
"""
Filters out sequences with too much ambiguity as defined by the method
parameters.
:type records: list
:param records: A list of sequences
:type repeats: int
:param repeats: Defines the number of repeated N that trigger truncat... | [
"Filters",
"out",
"sequences",
"with",
"too",
"much",
"ambiguity",
"as",
"defined",
"by",
"the",
"method",
"parameters",
"."
] | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/filter_ambiguity.py#L16-L41 | [
"def",
"filter_ambiguity",
"(",
"records",
",",
"percent",
"=",
"0.5",
")",
":",
"# , repeats=6)",
"seqs",
"=",
"[",
"]",
"# Ns = ''.join(['N' for _ in range(repeats)])",
"count",
"=",
"0",
"for",
"record",
"in",
"records",
":",
"if",
"record",
".",
"seq",
"."... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | Tree._parse | :param root: Tree node.
:param line: String to parse.
:param idx: Global counter of characters parsed.
:return: (list of parsed graphemes, incremented character count) | src/segments/tree.py | def _parse(self, root, line, idx):
"""
:param root: Tree node.
:param line: String to parse.
:param idx: Global counter of characters parsed.
:return: (list of parsed graphemes, incremented character count)
"""
# Base (or degenerate..) case.
if len(line) =... | def _parse(self, root, line, idx):
"""
:param root: Tree node.
:param line: String to parse.
:param idx: Global counter of characters parsed.
:return: (list of parsed graphemes, incremented character count)
"""
# Base (or degenerate..) case.
if len(line) =... | [
":",
"param",
"root",
":",
"Tree",
"node",
".",
":",
"param",
"line",
":",
"String",
"to",
"parse",
".",
":",
"param",
"idx",
":",
"Global",
"counter",
"of",
"characters",
"parsed",
".",
":",
"return",
":",
"(",
"list",
"of",
"parsed",
"graphemes",
"... | cldf/segments | python | https://github.com/cldf/segments/blob/9136a4ec89555bf9b574399ffbb07f3cc9a9f45f/src/segments/tree.py#L42-L70 | [
"def",
"_parse",
"(",
"self",
",",
"root",
",",
"line",
",",
"idx",
")",
":",
"# Base (or degenerate..) case.",
"if",
"len",
"(",
"line",
")",
"==",
"0",
":",
"return",
"[",
"]",
",",
"idx",
"parse",
"=",
"[",
"]",
"curr",
"=",
"0",
"node",
"=",
... | 9136a4ec89555bf9b574399ffbb07f3cc9a9f45f |
train | package_existent | Search package.
* :class:`bootstrap_py.exceptions.Conflict` exception occurs
when user specified name has already existed.
* :class:`bootstrap_py.exceptions.BackendFailure` exception occurs
when PyPI service is down.
:param str name: package name | bootstrap_py/pypi.py | def package_existent(name):
"""Search package.
* :class:`bootstrap_py.exceptions.Conflict` exception occurs
when user specified name has already existed.
* :class:`bootstrap_py.exceptions.BackendFailure` exception occurs
when PyPI service is down.
:param str name: package name
"""
... | def package_existent(name):
"""Search package.
* :class:`bootstrap_py.exceptions.Conflict` exception occurs
when user specified name has already existed.
* :class:`bootstrap_py.exceptions.BackendFailure` exception occurs
when PyPI service is down.
:param str name: package name
"""
... | [
"Search",
"package",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/pypi.py#L12-L33 | [
"def",
"package_existent",
"(",
"name",
")",
":",
"try",
":",
"response",
"=",
"requests",
".",
"get",
"(",
"PYPI_URL",
".",
"format",
"(",
"name",
")",
")",
"if",
"response",
".",
"ok",
":",
"msg",
"=",
"(",
"'[error] \"{0}\" is registered already in PyPI.\... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | write_relative_abundance | Given a BIOM table, calculate per-sample relative abundance for
each OTU and write out to a tab-separated file listing OTUs as
rows and Samples as columns.
:type biom: biom object
:param biom: BIOM-formatted OTU/Sample abundance data
:type out_fn: str
:param out_fn: The full path to the desired ... | bin/biom_relative_abundance.py | def write_relative_abundance(rel_abd, biomf, out_fn, sort_by=None):
"""
Given a BIOM table, calculate per-sample relative abundance for
each OTU and write out to a tab-separated file listing OTUs as
rows and Samples as columns.
:type biom: biom object
:param biom: BIOM-formatted OTU/Sample abund... | def write_relative_abundance(rel_abd, biomf, out_fn, sort_by=None):
"""
Given a BIOM table, calculate per-sample relative abundance for
each OTU and write out to a tab-separated file listing OTUs as
rows and Samples as columns.
:type biom: biom object
:param biom: BIOM-formatted OTU/Sample abund... | [
"Given",
"a",
"BIOM",
"table",
"calculate",
"per",
"-",
"sample",
"relative",
"abundance",
"for",
"each",
"OTU",
"and",
"write",
"out",
"to",
"a",
"tab",
"-",
"separated",
"file",
"listing",
"OTUs",
"as",
"rows",
"and",
"Samples",
"as",
"columns",
".",
"... | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/biom_relative_abundance.py#L15-L39 | [
"def",
"write_relative_abundance",
"(",
"rel_abd",
",",
"biomf",
",",
"out_fn",
",",
"sort_by",
"=",
"None",
")",
":",
"with",
"open",
"(",
"out_fn",
",",
"'w'",
")",
"as",
"out_f",
":",
"sids",
"=",
"sorted",
"(",
"set",
"(",
"biomf",
".",
"ids",
"(... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | append_index_id | add index to id to make it unique wrt ids | ctbBio/nr_fasta.py | def append_index_id(id, ids):
"""
add index to id to make it unique wrt ids
"""
index = 1
mod = '%s_%s' % (id, index)
while mod in ids:
index += 1
mod = '%s_%s' % (id, index)
ids.append(mod)
return mod, ids | def append_index_id(id, ids):
"""
add index to id to make it unique wrt ids
"""
index = 1
mod = '%s_%s' % (id, index)
while mod in ids:
index += 1
mod = '%s_%s' % (id, index)
ids.append(mod)
return mod, ids | [
"add",
"index",
"to",
"id",
"to",
"make",
"it",
"unique",
"wrt",
"ids"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/nr_fasta.py#L11-L21 | [
"def",
"append_index_id",
"(",
"id",
",",
"ids",
")",
":",
"index",
"=",
"1",
"mod",
"=",
"'%s_%s'",
"%",
"(",
"id",
",",
"index",
")",
"while",
"mod",
"in",
"ids",
":",
"index",
"+=",
"1",
"mod",
"=",
"'%s_%s'",
"%",
"(",
"id",
",",
"index",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | de_rep | de-replicate fastas based on sequence names | ctbBio/nr_fasta.py | def de_rep(fastas, append_index, return_original = False):
"""
de-replicate fastas based on sequence names
"""
ids = []
for fasta in fastas:
for seq in parse_fasta(fasta):
header = seq[0].split('>')[1].split()
id = header[0]
if id not in ids:
... | def de_rep(fastas, append_index, return_original = False):
"""
de-replicate fastas based on sequence names
"""
ids = []
for fasta in fastas:
for seq in parse_fasta(fasta):
header = seq[0].split('>')[1].split()
id = header[0]
if id not in ids:
... | [
"de",
"-",
"replicate",
"fastas",
"based",
"on",
"sequence",
"names"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/nr_fasta.py#L23-L43 | [
"def",
"de_rep",
"(",
"fastas",
",",
"append_index",
",",
"return_original",
"=",
"False",
")",
":",
"ids",
"=",
"[",
"]",
"for",
"fasta",
"in",
"fastas",
":",
"for",
"seq",
"in",
"parse_fasta",
"(",
"fasta",
")",
":",
"header",
"=",
"seq",
"[",
"0",... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | get | Request data associated with `postcode`.
:param postcode: the postcode to search for. The postcode may
contain spaces (they will be removed).
:returns: a dict of the nearest postcode's data or None if no
postcode data is found. | postcodes.py | def get(postcode):
"""
Request data associated with `postcode`.
:param postcode: the postcode to search for. The postcode may
contain spaces (they will be removed).
:returns: a dict of the nearest postcode's data or None if no
postcode data is found.
"""
po... | def get(postcode):
"""
Request data associated with `postcode`.
:param postcode: the postcode to search for. The postcode may
contain spaces (they will be removed).
:returns: a dict of the nearest postcode's data or None if no
postcode data is found.
"""
po... | [
"Request",
"data",
"associated",
"with",
"postcode",
"."
] | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L22-L34 | [
"def",
"get",
"(",
"postcode",
")",
":",
"postcode",
"=",
"quote",
"(",
"postcode",
".",
"replace",
"(",
"' '",
",",
"''",
")",
")",
"url",
"=",
"'%s/postcode/%s.json'",
"%",
"(",
"END_POINT",
",",
"postcode",
")",
"return",
"_get_json_resp",
"(",
"url",... | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | get_from_postcode | Request all postcode data within `distance` miles of `postcode`.
:param postcode: the postcode to search for. The postcode may
contain spaces (they will be removed).
:param distance: distance in miles to `postcode`.
:returns: a list of dicts containing postcode data within the
... | postcodes.py | def get_from_postcode(postcode, distance):
"""
Request all postcode data within `distance` miles of `postcode`.
:param postcode: the postcode to search for. The postcode may
contain spaces (they will be removed).
:param distance: distance in miles to `postcode`.
:returns: a ... | def get_from_postcode(postcode, distance):
"""
Request all postcode data within `distance` miles of `postcode`.
:param postcode: the postcode to search for. The postcode may
contain spaces (they will be removed).
:param distance: distance in miles to `postcode`.
:returns: a ... | [
"Request",
"all",
"postcode",
"data",
"within",
"distance",
"miles",
"of",
"postcode",
"."
] | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L56-L69 | [
"def",
"get_from_postcode",
"(",
"postcode",
",",
"distance",
")",
":",
"postcode",
"=",
"quote",
"(",
"postcode",
".",
"replace",
"(",
"' '",
",",
"''",
")",
")",
"return",
"_get_from",
"(",
"distance",
",",
"'postcode=%s'",
"%",
"postcode",
")"
] | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | PostCoder._check_point | Checks if latitude and longitude correct | postcodes.py | def _check_point(self, lat, lng):
""" Checks if latitude and longitude correct """
if abs(lat) > 90 or abs(lng) > 180:
msg = "Illegal lat and/or lng, (%s, %s) provided." % (lat, lng)
raise IllegalPointException(msg) | def _check_point(self, lat, lng):
""" Checks if latitude and longitude correct """
if abs(lat) > 90 or abs(lng) > 180:
msg = "Illegal lat and/or lng, (%s, %s) provided." % (lat, lng)
raise IllegalPointException(msg) | [
"Checks",
"if",
"latitude",
"and",
"longitude",
"correct"
] | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L123-L127 | [
"def",
"_check_point",
"(",
"self",
",",
"lat",
",",
"lng",
")",
":",
"if",
"abs",
"(",
"lat",
")",
">",
"90",
"or",
"abs",
"(",
"lng",
")",
">",
"180",
":",
"msg",
"=",
"\"Illegal lat and/or lng, (%s, %s) provided.\"",
"%",
"(",
"lat",
",",
"lng",
"... | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | PostCoder._lookup | Checks for cached responses, before requesting from
web-service | postcodes.py | def _lookup(self, skip_cache, fun, *args, **kwargs):
"""
Checks for cached responses, before requesting from
web-service
"""
if args not in self.cache or skip_cache:
self.cache[args] = fun(*args, **kwargs)
return self.cache[args] | def _lookup(self, skip_cache, fun, *args, **kwargs):
"""
Checks for cached responses, before requesting from
web-service
"""
if args not in self.cache or skip_cache:
self.cache[args] = fun(*args, **kwargs)
return self.cache[args] | [
"Checks",
"for",
"cached",
"responses",
"before",
"requesting",
"from",
"web",
"-",
"service"
] | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L129-L136 | [
"def",
"_lookup",
"(",
"self",
",",
"skip_cache",
",",
"fun",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"args",
"not",
"in",
"self",
".",
"cache",
"or",
"skip_cache",
":",
"self",
".",
"cache",
"[",
"args",
"]",
"=",
"fun",
"(",
... | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | PostCoder.get | Calls `postcodes.get` and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an explicit request.
Given postcode data doesn't really change,
it's unlike... | postcodes.py | def get(self, postcode, skip_cache=False):
"""
Calls `postcodes.get` and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an explicit request.
Given postcode data... | def get(self, postcode, skip_cache=False):
"""
Calls `postcodes.get` and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an explicit request.
Given postcode data... | [
"Calls",
"postcodes",
".",
"get",
"and",
"by",
"default",
"utilises",
"a",
"local",
"cache",
".",
":",
"param",
"skip_cache",
":",
"optional",
"argument",
"specifying",
"whether",
"to",
"skip",
"the",
"cache",
"and",
"make",
"an",
"explicit",
"request",
".",... | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L138-L150 | [
"def",
"get",
"(",
"self",
",",
"postcode",
",",
"skip_cache",
"=",
"False",
")",
":",
"# remove spaces and change case here due to caching",
"postcode",
"=",
"postcode",
".",
"lower",
"(",
")",
".",
"replace",
"(",
"' '",
",",
"''",
")",
"return",
"self",
"... | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | PostCoder.get_nearest | Calls `postcodes.get_nearest` but checks correctness of `lat`
and `long`, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an explicit request.
:raises IllegalPointException: if the latitude o... | postcodes.py | def get_nearest(self, lat, lng, skip_cache=False):
"""
Calls `postcodes.get_nearest` but checks correctness of `lat`
and `long`, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an exp... | def get_nearest(self, lat, lng, skip_cache=False):
"""
Calls `postcodes.get_nearest` but checks correctness of `lat`
and `long`, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an exp... | [
"Calls",
"postcodes",
".",
"get_nearest",
"but",
"checks",
"correctness",
"of",
"lat",
"and",
"long",
"and",
"by",
"default",
"utilises",
"a",
"local",
"cache",
"."
] | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L152-L167 | [
"def",
"get_nearest",
"(",
"self",
",",
"lat",
",",
"lng",
",",
"skip_cache",
"=",
"False",
")",
":",
"lat",
",",
"lng",
"=",
"float",
"(",
"lat",
")",
",",
"float",
"(",
"lng",
")",
"self",
".",
"_check_point",
"(",
"lat",
",",
"lng",
")",
"retu... | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | PostCoder.get_from_postcode | Calls `postcodes.get_from_postcode` but checks correctness of
`distance`, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an explicit request.
:raises IllegalPointException: if the latitude o... | postcodes.py | def get_from_postcode(self, postcode, distance, skip_cache=False):
"""
Calls `postcodes.get_from_postcode` but checks correctness of
`distance`, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache ... | def get_from_postcode(self, postcode, distance, skip_cache=False):
"""
Calls `postcodes.get_from_postcode` but checks correctness of
`distance`, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache ... | [
"Calls",
"postcodes",
".",
"get_from_postcode",
"but",
"checks",
"correctness",
"of",
"distance",
"and",
"by",
"default",
"utilises",
"a",
"local",
"cache",
"."
] | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L169-L189 | [
"def",
"get_from_postcode",
"(",
"self",
",",
"postcode",
",",
"distance",
",",
"skip_cache",
"=",
"False",
")",
":",
"distance",
"=",
"float",
"(",
"distance",
")",
"if",
"distance",
"<",
"0",
":",
"raise",
"IllegalDistanceException",
"(",
"\"Distance must no... | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | PostCoder.get_from_geo | Calls `postcodes.get_from_geo` but checks the correctness of
all arguments, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and make an explicit request.
:raises IllegalPointException: if the latitude... | postcodes.py | def get_from_geo(self, lat, lng, distance, skip_cache=False):
"""
Calls `postcodes.get_from_geo` but checks the correctness of
all arguments, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and... | def get_from_geo(self, lat, lng, distance, skip_cache=False):
"""
Calls `postcodes.get_from_geo` but checks the correctness of
all arguments, and by default utilises a local cache.
:param skip_cache: optional argument specifying whether to skip
the cache and... | [
"Calls",
"postcodes",
".",
"get_from_geo",
"but",
"checks",
"the",
"correctness",
"of",
"all",
"arguments",
"and",
"by",
"default",
"utilises",
"a",
"local",
"cache",
"."
] | e-dard/postcodes | python | https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L191-L210 | [
"def",
"get_from_geo",
"(",
"self",
",",
"lat",
",",
"lng",
",",
"distance",
",",
"skip_cache",
"=",
"False",
")",
":",
"# remove spaces and change case here due to caching",
"lat",
",",
"lng",
",",
"distance",
"=",
"float",
"(",
"lat",
")",
",",
"float",
"(... | d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005 |
train | insertions_from_masked | get coordinates of insertions from insertion-masked sequence | ctbBio/rRNA_insertions.py | def insertions_from_masked(seq):
"""
get coordinates of insertions from insertion-masked sequence
"""
insertions = []
prev = True
for i, base in enumerate(seq):
if base.isupper() and prev is True:
insertions.append([])
prev = False
elif base.islower():
... | def insertions_from_masked(seq):
"""
get coordinates of insertions from insertion-masked sequence
"""
insertions = []
prev = True
for i, base in enumerate(seq):
if base.isupper() and prev is True:
insertions.append([])
prev = False
elif base.islower():
... | [
"get",
"coordinates",
"of",
"insertions",
"from",
"insertion",
"-",
"masked",
"sequence"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L15-L28 | [
"def",
"insertions_from_masked",
"(",
"seq",
")",
":",
"insertions",
"=",
"[",
"]",
"prev",
"=",
"True",
"for",
"i",
",",
"base",
"in",
"enumerate",
"(",
"seq",
")",
":",
"if",
"base",
".",
"isupper",
"(",
")",
"and",
"prev",
"is",
"True",
":",
"in... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | analyze_fa | analyze fa (names, insertions) and convert fasta to prodigal/cmscan safe file
- find insertions (masked sequence)
- make upper case
- assign names to id number | ctbBio/rRNA_insertions.py | def analyze_fa(fa):
"""
analyze fa (names, insertions) and convert fasta to prodigal/cmscan safe file
- find insertions (masked sequence)
- make upper case
- assign names to id number
"""
if fa.name == '<stdin>':
safe = 'temp.id'
else:
safe = '%s.id' % (fa.name)
safe ... | def analyze_fa(fa):
"""
analyze fa (names, insertions) and convert fasta to prodigal/cmscan safe file
- find insertions (masked sequence)
- make upper case
- assign names to id number
"""
if fa.name == '<stdin>':
safe = 'temp.id'
else:
safe = '%s.id' % (fa.name)
safe ... | [
"analyze",
"fa",
"(",
"names",
"insertions",
")",
"and",
"convert",
"fasta",
"to",
"prodigal",
"/",
"cmscan",
"safe",
"file",
"-",
"find",
"insertions",
"(",
"masked",
"sequence",
")",
"-",
"make",
"upper",
"case",
"-",
"assign",
"names",
"to",
"id",
"nu... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L30-L62 | [
"def",
"analyze_fa",
"(",
"fa",
")",
":",
"if",
"fa",
".",
"name",
"==",
"'<stdin>'",
":",
"safe",
"=",
"'temp.id'",
"else",
":",
"safe",
"=",
"'%s.id'",
"%",
"(",
"fa",
".",
"name",
")",
"safe",
"=",
"open",
"(",
"safe",
",",
"'w'",
")",
"sequen... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | seq_info | get insertion information from header | ctbBio/rRNA_insertions.py | def seq_info(names, id2names, insertions, sequences):
"""
get insertion information from header
"""
seqs = {} # seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
for name in names:
id = id2names[name]
gene = name.split('fromHMM::', 1)[0].rs... | def seq_info(names, id2names, insertions, sequences):
"""
get insertion information from header
"""
seqs = {} # seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
for name in names:
id = id2names[name]
gene = name.split('fromHMM::', 1)[0].rs... | [
"get",
"insertion",
"information",
"from",
"header"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L64-L86 | [
"def",
"seq_info",
"(",
"names",
",",
"id2names",
",",
"insertions",
",",
"sequences",
")",
":",
"seqs",
"=",
"{",
"}",
"# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]",
"for",
"name",
"in",
"names",
":",
"id",
"=",
"id... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | check_overlap | make sure thresh % feature is contained within insertion | ctbBio/rRNA_insertions.py | def check_overlap(pos, ins, thresh):
"""
make sure thresh % feature is contained within insertion
"""
ins_pos = ins[0]
ins_len = ins[2]
ol = overlap(ins_pos, pos)
feat_len = pos[1] - pos[0] + 1
# print float(ol) / float(feat_len)
if float(ol) / float(feat_len) >= thresh:
retur... | def check_overlap(pos, ins, thresh):
"""
make sure thresh % feature is contained within insertion
"""
ins_pos = ins[0]
ins_len = ins[2]
ol = overlap(ins_pos, pos)
feat_len = pos[1] - pos[0] + 1
# print float(ol) / float(feat_len)
if float(ol) / float(feat_len) >= thresh:
retur... | [
"make",
"sure",
"thresh",
"%",
"feature",
"is",
"contained",
"within",
"insertion"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L91-L102 | [
"def",
"check_overlap",
"(",
"pos",
",",
"ins",
",",
"thresh",
")",
":",
"ins_pos",
"=",
"ins",
"[",
"0",
"]",
"ins_len",
"=",
"ins",
"[",
"2",
"]",
"ol",
"=",
"overlap",
"(",
"ins_pos",
",",
"pos",
")",
"feat_len",
"=",
"pos",
"[",
"1",
"]",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | find_orfs | find orfs and see if they overlap with insertions
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]] | ctbBio/rRNA_insertions.py | def find_orfs(fa, seqs):
"""
find orfs and see if they overlap with insertions
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
"""
faa = '%s.prodigal.faa' % (fa)
fna = '%s.prodigal.fna' % (fa)
gbk = '%s.prodigal.gbk' % (fa)
if os.path.exist... | def find_orfs(fa, seqs):
"""
find orfs and see if they overlap with insertions
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
"""
faa = '%s.prodigal.faa' % (fa)
fna = '%s.prodigal.fna' % (fa)
gbk = '%s.prodigal.gbk' % (fa)
if os.path.exist... | [
"find",
"orfs",
"and",
"see",
"if",
"they",
"overlap",
"with",
"insertions",
"#",
"seqs",
"[",
"id",
"]",
"=",
"[",
"gene",
"model",
"[[",
"i",
"-",
"gene_pos",
"i",
"-",
"model_pos",
"i",
"-",
"length",
"iseq",
"[",
"orfs",
"]",
"[",
"introns",
"]... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L104-L126 | [
"def",
"find_orfs",
"(",
"fa",
",",
"seqs",
")",
":",
"faa",
"=",
"'%s.prodigal.faa'",
"%",
"(",
"fa",
")",
"fna",
"=",
"'%s.prodigal.fna'",
"%",
"(",
"fa",
")",
"gbk",
"=",
"'%s.prodigal.gbk'",
"%",
"(",
"fa",
")",
"if",
"os",
".",
"path",
".",
"e... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | find_introns | find introns by searching Rfam intron databse using cmscan
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]] | ctbBio/rRNA_insertions.py | def find_introns(fa, seqs, sequences, threads):
"""
find introns by searching Rfam intron databse using cmscan
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
"""
db = '%s/rfam/Rfam.cm.1_1.introns' % (os.environ['databases'])
out = '%s.rfam-introns... | def find_introns(fa, seqs, sequences, threads):
"""
find introns by searching Rfam intron databse using cmscan
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
"""
db = '%s/rfam/Rfam.cm.1_1.introns' % (os.environ['databases'])
out = '%s.rfam-introns... | [
"find",
"introns",
"by",
"searching",
"Rfam",
"intron",
"databse",
"using",
"cmscan",
"#",
"seqs",
"[",
"id",
"]",
"=",
"[",
"gene",
"model",
"[[",
"i",
"-",
"gene_pos",
"i",
"-",
"model_pos",
"i",
"-",
"length",
"iseq",
"[",
"orfs",
"]",
"[",
"intro... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L128-L156 | [
"def",
"find_introns",
"(",
"fa",
",",
"seqs",
",",
"sequences",
",",
"threads",
")",
":",
"db",
"=",
"'%s/rfam/Rfam.cm.1_1.introns'",
"%",
"(",
"os",
".",
"environ",
"[",
"'databases'",
"]",
")",
"out",
"=",
"'%s.rfam-introns.cmscan'",
"%",
"(",
"fa",
")"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | annotate_orfs | search orfs against pfam
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?, {orf: annotations}], ...]] | ctbBio/rRNA_insertions.py | def annotate_orfs(fa, seqs, threads, threshold = 1e-6):
"""
search orfs against pfam
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?, {orf: annotations}], ...]]
"""
db = '%s/pfam/Pfam-A.hmm' % os.environ['databases']
base = fa.rsplit('.', ... | def annotate_orfs(fa, seqs, threads, threshold = 1e-6):
"""
search orfs against pfam
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?, {orf: annotations}], ...]]
"""
db = '%s/pfam/Pfam-A.hmm' % os.environ['databases']
base = fa.rsplit('.', ... | [
"search",
"orfs",
"against",
"pfam",
"#",
"seqs",
"[",
"id",
"]",
"=",
"[",
"gene",
"model",
"[[",
"i",
"-",
"gene_pos",
"i",
"-",
"model_pos",
"i",
"-",
"length",
"iseq",
"[",
"orfs",
"]",
"[",
"introns",
"]",
"orfs?",
"introns?",
"{",
"orf",
":",... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L158-L195 | [
"def",
"annotate_orfs",
"(",
"fa",
",",
"seqs",
",",
"threads",
",",
"threshold",
"=",
"1e-6",
")",
":",
"db",
"=",
"'%s/pfam/Pfam-A.hmm'",
"%",
"os",
".",
"environ",
"[",
"'databases'",
"]",
"base",
"=",
"fa",
".",
"rsplit",
"(",
"'.'",
",",
"1",
")... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | analyze_insertions | - find ORFs using Prodigal
- find introns using cmscan (vs Rfam intron database)
- check that ORFs and intron overlap with insertion region
- plot insertion length versus model position for each insertion (based on insertion type) | ctbBio/rRNA_insertions.py | def analyze_insertions(fa, threads = 6):
"""
- find ORFs using Prodigal
- find introns using cmscan (vs Rfam intron database)
- check that ORFs and intron overlap with insertion region
- plot insertion length versus model position for each insertion (based on insertion type)
"""
safe, sequen... | def analyze_insertions(fa, threads = 6):
"""
- find ORFs using Prodigal
- find introns using cmscan (vs Rfam intron database)
- check that ORFs and intron overlap with insertion region
- plot insertion length versus model position for each insertion (based on insertion type)
"""
safe, sequen... | [
"-",
"find",
"ORFs",
"using",
"Prodigal",
"-",
"find",
"introns",
"using",
"cmscan",
"(",
"vs",
"Rfam",
"intron",
"database",
")",
"-",
"check",
"that",
"ORFs",
"and",
"intron",
"overlap",
"with",
"insertion",
"region",
"-",
"plot",
"insertion",
"length",
... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L197-L210 | [
"def",
"analyze_insertions",
"(",
"fa",
",",
"threads",
"=",
"6",
")",
":",
"safe",
",",
"sequences",
",",
"id2name",
",",
"names",
",",
"insertions",
"=",
"analyze_fa",
"(",
"fa",
")",
"seqs",
"=",
"seq_info",
"(",
"names",
",",
"id2name",
",",
"inser... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | seqs2bool | convert orf and intron information to boolean
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?], ...]] | ctbBio/rRNA_insertions.py | def seqs2bool(seqs):
"""
convert orf and intron information to boolean
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?], ...]]
"""
for seq in s... | def seqs2bool(seqs):
"""
convert orf and intron information to boolean
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?], ...]]
"""
for seq in s... | [
"convert",
"orf",
"and",
"intron",
"information",
"to",
"boolean",
"#",
"seqs",
"[",
"id",
"]",
"=",
"[",
"gene",
"model",
"[[",
"i",
"-",
"gene_pos",
"i",
"-",
"model_pos",
"i",
"-",
"length",
"iseq",
"[",
"orfs",
"]",
"[",
"introns",
"]]",
"...",
... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L212-L229 | [
"def",
"seqs2bool",
"(",
"seqs",
")",
":",
"for",
"seq",
"in",
"seqs",
":",
"for",
"i",
",",
"ins",
"in",
"enumerate",
"(",
"seqs",
"[",
"seq",
"]",
"[",
"2",
"]",
")",
":",
"if",
"len",
"(",
"ins",
"[",
"4",
"]",
")",
">",
"0",
":",
"ins",... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | print_table | print table of results
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?], ...]] | ctbBio/rRNA_insertions.py | def print_table(seqs, id2name, name):
"""
print table of results
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?], ...]]
"""
itable = open('%s.itable' % (name.rsplit('.', 1)[0]), 'w')
print('\t'.join(['#sequence', 'gene', 'model', 'inserti... | def print_table(seqs, id2name, name):
"""
print table of results
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?], ...]]
"""
itable = open('%s.itable' % (name.rsplit('.', 1)[0]), 'w')
print('\t'.join(['#sequence', 'gene', 'model', 'inserti... | [
"print",
"table",
"of",
"results",
"#",
"seqs",
"[",
"id",
"]",
"=",
"[",
"gene",
"model",
"[[",
"i",
"-",
"gene_pos",
"i",
"-",
"model_pos",
"i",
"-",
"length",
"iseq",
"[",
"orfs",
"]",
"[",
"introns",
"]",
"orfs?",
"introns?",
"]",
"...",
"]]"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L231-L261 | [
"def",
"print_table",
"(",
"seqs",
",",
"id2name",
",",
"name",
")",
":",
"itable",
"=",
"open",
"(",
"'%s.itable'",
"%",
"(",
"name",
".",
"rsplit",
"(",
"'.'",
",",
"1",
")",
"[",
"0",
"]",
")",
",",
"'w'",
")",
"print",
"(",
"'\\t'",
".",
"j... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | print_seqs | print fasta of introns and ORFs
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?, [orf annotations]], ...]] | ctbBio/rRNA_insertions.py | def print_seqs(seqs, id2name, name):
"""
print fasta of introns and ORFs
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?, [orf annotations]], ...]]
"""
orfs = open('%s.orfs.faa' % (name.rsplit('.', 1)[0]), 'w')
introns = open('%s.introns.f... | def print_seqs(seqs, id2name, name):
"""
print fasta of introns and ORFs
# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns], orfs?, introns?, [orf annotations]], ...]]
"""
orfs = open('%s.orfs.faa' % (name.rsplit('.', 1)[0]), 'w')
introns = open('%s.introns.f... | [
"print",
"fasta",
"of",
"introns",
"and",
"ORFs",
"#",
"seqs",
"[",
"id",
"]",
"=",
"[",
"gene",
"model",
"[[",
"i",
"-",
"gene_pos",
"i",
"-",
"model_pos",
"i",
"-",
"length",
"iseq",
"[",
"orfs",
"]",
"[",
"introns",
"]",
"orfs?",
"introns?",
"["... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L263-L303 | [
"def",
"print_seqs",
"(",
"seqs",
",",
"id2name",
",",
"name",
")",
":",
"orfs",
"=",
"open",
"(",
"'%s.orfs.faa'",
"%",
"(",
"name",
".",
"rsplit",
"(",
"'.'",
",",
"1",
")",
"[",
"0",
"]",
")",
",",
"'w'",
")",
"introns",
"=",
"open",
"(",
"'... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | max_insertion | length of largest insertion | ctbBio/rRNA_insertions.py | def max_insertion(seqs, gene, domain):
"""
length of largest insertion
"""
seqs = [i[2] for i in list(seqs.values()) if i[2] != [] and i[0] == gene and i[1] == domain]
lengths = []
for seq in seqs:
for ins in seq:
lengths.append(int(ins[2]))
if lengths == []:
retu... | def max_insertion(seqs, gene, domain):
"""
length of largest insertion
"""
seqs = [i[2] for i in list(seqs.values()) if i[2] != [] and i[0] == gene and i[1] == domain]
lengths = []
for seq in seqs:
for ins in seq:
lengths.append(int(ins[2]))
if lengths == []:
retu... | [
"length",
"of",
"largest",
"insertion"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L305-L316 | [
"def",
"max_insertion",
"(",
"seqs",
",",
"gene",
",",
"domain",
")",
":",
"seqs",
"=",
"[",
"i",
"[",
"2",
"]",
"for",
"i",
"in",
"list",
"(",
"seqs",
".",
"values",
"(",
")",
")",
"if",
"i",
"[",
"2",
"]",
"!=",
"[",
"]",
"and",
"i",
"[",... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | model_length | get length of model | ctbBio/rRNA_insertions.py | def model_length(gene, domain):
"""
get length of model
"""
if gene == '16S':
domain2max = {'E_coli_K12': int(1538), 'bacteria': int(1689), 'archaea': int(1563), 'eukarya': int(2652)}
return domain2max[domain]
elif gene == '23S':
domain2max = {'E_coli_K12': int(2903), 'bacter... | def model_length(gene, domain):
"""
get length of model
"""
if gene == '16S':
domain2max = {'E_coli_K12': int(1538), 'bacteria': int(1689), 'archaea': int(1563), 'eukarya': int(2652)}
return domain2max[domain]
elif gene == '23S':
domain2max = {'E_coli_K12': int(2903), 'bacter... | [
"get",
"length",
"of",
"model"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L318-L330 | [
"def",
"model_length",
"(",
"gene",
",",
"domain",
")",
":",
"if",
"gene",
"==",
"'16S'",
":",
"domain2max",
"=",
"{",
"'E_coli_K12'",
":",
"int",
"(",
"1538",
")",
",",
"'bacteria'",
":",
"int",
"(",
"1689",
")",
",",
"'archaea'",
":",
"int",
"(",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | setup_markers | setup unique marker for every orf annotation
- change size if necessary | ctbBio/rRNA_insertions.py | def setup_markers(seqs):
"""
setup unique marker for every orf annotation
- change size if necessary
"""
family2marker = {} # family2marker[family] = [marker, size]
markers = cycle(['^', 'p', '*', '+', 'x', 'd', '|', 'v', '>', '<', '8'])
size = 60
families = []
for seq in list(seqs.v... | def setup_markers(seqs):
"""
setup unique marker for every orf annotation
- change size if necessary
"""
family2marker = {} # family2marker[family] = [marker, size]
markers = cycle(['^', 'p', '*', '+', 'x', 'd', '|', 'v', '>', '<', '8'])
size = 60
families = []
for seq in list(seqs.v... | [
"setup",
"unique",
"marker",
"for",
"every",
"orf",
"annotation",
"-",
"change",
"size",
"if",
"necessary"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L332-L351 | [
"def",
"setup_markers",
"(",
"seqs",
")",
":",
"family2marker",
"=",
"{",
"}",
"# family2marker[family] = [marker, size]",
"markers",
"=",
"cycle",
"(",
"[",
"'^'",
",",
"'p'",
",",
"'*'",
",",
"'+'",
",",
"'x'",
",",
"'d'",
",",
"'|'",
",",
"'v'",
",",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | plot_insertions | plot insertions wrt model positions
2 panels:
1. insertions with ORF
- triangle if has intron
- circle if no intron
2. insertion does not have ORF
- triangle if has intron
- circle if no intron
*3. conservation of sequence in model
*4. ... | ctbBio/rRNA_insertions.py | def plot_insertions(fname, seqs, gene, domain, tax, id2name):
"""
plot insertions wrt model positions
2 panels:
1. insertions with ORF
- triangle if has intron
- circle if no intron
2. insertion does not have ORF
- triangle if has intron
- circ... | def plot_insertions(fname, seqs, gene, domain, tax, id2name):
"""
plot insertions wrt model positions
2 panels:
1. insertions with ORF
- triangle if has intron
- circle if no intron
2. insertion does not have ORF
- triangle if has intron
- circ... | [
"plot",
"insertions",
"wrt",
"model",
"positions",
"2",
"panels",
":",
"1",
".",
"insertions",
"with",
"ORF",
"-",
"triangle",
"if",
"has",
"intron",
"-",
"circle",
"if",
"no",
"intron",
"2",
".",
"insertion",
"does",
"not",
"have",
"ORF",
"-",
"triangle... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L353-L463 | [
"def",
"plot_insertions",
"(",
"fname",
",",
"seqs",
",",
"gene",
",",
"domain",
",",
"tax",
",",
"id2name",
")",
":",
"# import",
"import",
"matplotlib",
"import",
"matplotlib",
".",
"pyplot",
"as",
"plt",
"import",
"numpy",
"as",
"np",
"from",
"matplotli... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | plot_by_gene_and_domain | plot insertions for each gene and domain | ctbBio/rRNA_insertions.py | def plot_by_gene_and_domain(name, seqs, tax, id2name):
"""
plot insertions for each gene and domain
"""
for gene in set([seq[0] for seq in list(seqs.values())]):
for domain in set([seq[1] for seq in list(seqs.values())]):
plot_insertions(name, seqs, gene, domain, tax, id2name) | def plot_by_gene_and_domain(name, seqs, tax, id2name):
"""
plot insertions for each gene and domain
"""
for gene in set([seq[0] for seq in list(seqs.values())]):
for domain in set([seq[1] for seq in list(seqs.values())]):
plot_insertions(name, seqs, gene, domain, tax, id2name) | [
"plot",
"insertions",
"for",
"each",
"gene",
"and",
"domain"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L551-L557 | [
"def",
"plot_by_gene_and_domain",
"(",
"name",
",",
"seqs",
",",
"tax",
",",
"id2name",
")",
":",
"for",
"gene",
"in",
"set",
"(",
"[",
"seq",
"[",
"0",
"]",
"for",
"seq",
"in",
"list",
"(",
"seqs",
".",
"values",
"(",
")",
")",
"]",
")",
":",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | normalize_bit | normalize the bit score:
normalization factor = average max bit score for the two ORFs
normalized = bit score / normalization factor | ctbBio/neto.py | def normalize_bit(A, B, bit, id2desc):
"""
normalize the bit score:
normalization factor = average max bit score for the two ORFs
normalized = bit score / normalization factor
"""
Amax, Bmax = id2desc[A][-1], id2desc[B][-1]
norm_factor = float(numpy.average([Amax, Bmax]))
normalized = bi... | def normalize_bit(A, B, bit, id2desc):
"""
normalize the bit score:
normalization factor = average max bit score for the two ORFs
normalized = bit score / normalization factor
"""
Amax, Bmax = id2desc[A][-1], id2desc[B][-1]
norm_factor = float(numpy.average([Amax, Bmax]))
normalized = bi... | [
"normalize",
"the",
"bit",
"score",
":",
"normalization",
"factor",
"=",
"average",
"max",
"bit",
"score",
"for",
"the",
"two",
"ORFs",
"normalized",
"=",
"bit",
"score",
"/",
"normalization",
"factor"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L26-L35 | [
"def",
"normalize_bit",
"(",
"A",
",",
"B",
",",
"bit",
",",
"id2desc",
")",
":",
"Amax",
",",
"Bmax",
"=",
"id2desc",
"[",
"A",
"]",
"[",
"-",
"1",
"]",
",",
"id2desc",
"[",
"B",
"]",
"[",
"-",
"1",
"]",
"norm_factor",
"=",
"float",
"(",
"nu... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | get_descriptions | get the description for each ORF | ctbBio/neto.py | def get_descriptions(fastas):
"""
get the description for each ORF
"""
id2desc = {}
for fasta in fastas:
for seq in parse_fasta(fasta):
header = seq[0].split('>')[1].split(' ')
id = header[0]
if len(header) > 1:
desc = ' '.join(header[1:])... | def get_descriptions(fastas):
"""
get the description for each ORF
"""
id2desc = {}
for fasta in fastas:
for seq in parse_fasta(fasta):
header = seq[0].split('>')[1].split(' ')
id = header[0]
if len(header) > 1:
desc = ' '.join(header[1:])... | [
"get",
"the",
"description",
"for",
"each",
"ORF"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L37-L52 | [
"def",
"get_descriptions",
"(",
"fastas",
")",
":",
"id2desc",
"=",
"{",
"}",
"for",
"fasta",
"in",
"fastas",
":",
"for",
"seq",
"in",
"parse_fasta",
"(",
"fasta",
")",
":",
"header",
"=",
"seq",
"[",
"0",
"]",
".",
"split",
"(",
"'>'",
")",
"[",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | print_genome_matrix | optimize later? slow ...
should combine with calculate_threshold module | ctbBio/neto.py | def print_genome_matrix(hits, fastas, id2desc, file_name):
"""
optimize later? slow ...
should combine with calculate_threshold module
"""
out = open(file_name, 'w')
fastas = sorted(fastas)
print('## percent identity between genomes', file=out)
print('# - \t %s' % ('\t'.join(fastas)), fi... | def print_genome_matrix(hits, fastas, id2desc, file_name):
"""
optimize later? slow ...
should combine with calculate_threshold module
"""
out = open(file_name, 'w')
fastas = sorted(fastas)
print('## percent identity between genomes', file=out)
print('# - \t %s' % ('\t'.join(fastas)), fi... | [
"optimize",
"later?",
"slow",
"...",
"should",
"combine",
"with",
"calculate_threshold",
"module"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L140-L171 | [
"def",
"print_genome_matrix",
"(",
"hits",
",",
"fastas",
",",
"id2desc",
",",
"file_name",
")",
":",
"out",
"=",
"open",
"(",
"file_name",
",",
"'w'",
")",
"fastas",
"=",
"sorted",
"(",
"fastas",
")",
"print",
"(",
"'## percent identity between genomes'",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | self_compare | compare genome to self to get the best possible bit score for each ORF | ctbBio/neto.py | def self_compare(fastas, id2desc, algorithm):
"""
compare genome to self to get the best possible bit score for each ORF
"""
for fasta in fastas:
blast = open(search(fasta, fasta, method = algorithm, alignment = 'local'))
for hit in best_blast(blast, 1):
id, bit = hit[0].spli... | def self_compare(fastas, id2desc, algorithm):
"""
compare genome to self to get the best possible bit score for each ORF
"""
for fasta in fastas:
blast = open(search(fasta, fasta, method = algorithm, alignment = 'local'))
for hit in best_blast(blast, 1):
id, bit = hit[0].spli... | [
"compare",
"genome",
"to",
"self",
"to",
"get",
"the",
"best",
"possible",
"bit",
"score",
"for",
"each",
"ORF"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L240-L249 | [
"def",
"self_compare",
"(",
"fastas",
",",
"id2desc",
",",
"algorithm",
")",
":",
"for",
"fasta",
"in",
"fastas",
":",
"blast",
"=",
"open",
"(",
"search",
"(",
"fasta",
",",
"fasta",
",",
"method",
"=",
"algorithm",
",",
"alignment",
"=",
"'local'",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | compare_genomes | make all pairwise genome comparisons to get rbhs
rbh = {genome: {other_genome: {rbh_id: [rbh_match, pident, e, bit, norm_bit]]}} | ctbBio/neto.py | def compare_genomes(fastas, id2desc, algorithm):
"""
make all pairwise genome comparisons to get rbhs
rbh = {genome: {other_genome: {rbh_id: [rbh_match, pident, e, bit, norm_bit]]}}
"""
hits = {}
for pair in itertools.permutations(fastas, 2):
if pair[0] not in hits:
hits[pair... | def compare_genomes(fastas, id2desc, algorithm):
"""
make all pairwise genome comparisons to get rbhs
rbh = {genome: {other_genome: {rbh_id: [rbh_match, pident, e, bit, norm_bit]]}}
"""
hits = {}
for pair in itertools.permutations(fastas, 2):
if pair[0] not in hits:
hits[pair... | [
"make",
"all",
"pairwise",
"genome",
"comparisons",
"to",
"get",
"rbhs",
"rbh",
"=",
"{",
"genome",
":",
"{",
"other_genome",
":",
"{",
"rbh_id",
":",
"[",
"rbh_match",
"pident",
"e",
"bit",
"norm_bit",
"]]",
"}}"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L251-L274 | [
"def",
"compare_genomes",
"(",
"fastas",
",",
"id2desc",
",",
"algorithm",
")",
":",
"hits",
"=",
"{",
"}",
"for",
"pair",
"in",
"itertools",
".",
"permutations",
"(",
"fastas",
",",
"2",
")",
":",
"if",
"pair",
"[",
"0",
"]",
"not",
"in",
"hits",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | calc_thresholds | if thresholds are not specififed, calculate based on the distribution of normalized bit scores | ctbBio/neto.py | def calc_thresholds(rbh, file_name, thresholds = [False, False, False, False], stdevs = 2):
"""
if thresholds are not specififed, calculate based on the distribution of normalized bit scores
"""
calc_threshold = thresholds[-1]
norm_threshold = {}
for pair in itertools.permutations([i for i in rb... | def calc_thresholds(rbh, file_name, thresholds = [False, False, False, False], stdevs = 2):
"""
if thresholds are not specififed, calculate based on the distribution of normalized bit scores
"""
calc_threshold = thresholds[-1]
norm_threshold = {}
for pair in itertools.permutations([i for i in rb... | [
"if",
"thresholds",
"are",
"not",
"specififed",
"calculate",
"based",
"on",
"the",
"distribution",
"of",
"normalized",
"bit",
"scores"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L303-L352 | [
"def",
"calc_thresholds",
"(",
"rbh",
",",
"file_name",
",",
"thresholds",
"=",
"[",
"False",
",",
"False",
",",
"False",
",",
"False",
"]",
",",
"stdevs",
"=",
"2",
")",
":",
"calc_threshold",
"=",
"thresholds",
"[",
"-",
"1",
"]",
"norm_threshold",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | rbh_network | make the network based on rbhs and score thresholds | ctbBio/neto.py | def rbh_network(id2desc, rbh, file_name, thresholds = [False, False, False, False]):
"""
make the network based on rbhs and score thresholds
"""
g = nx.Graph() # network graph for storing rbhs
filtered = {}
e_thresh, bit_thresh, length_thresh, norm_thresh = thresholds
for genome in rbh:
... | def rbh_network(id2desc, rbh, file_name, thresholds = [False, False, False, False]):
"""
make the network based on rbhs and score thresholds
"""
g = nx.Graph() # network graph for storing rbhs
filtered = {}
e_thresh, bit_thresh, length_thresh, norm_thresh = thresholds
for genome in rbh:
... | [
"make",
"the",
"network",
"based",
"on",
"rbhs",
"and",
"score",
"thresholds"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L354-L414 | [
"def",
"rbh_network",
"(",
"id2desc",
",",
"rbh",
",",
"file_name",
",",
"thresholds",
"=",
"[",
"False",
",",
"False",
",",
"False",
",",
"False",
"]",
")",
":",
"g",
"=",
"nx",
".",
"Graph",
"(",
")",
"# network graph for storing rbhs",
"filtered",
"="... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | neto | make and split a rbh network | ctbBio/neto.py | def neto(fastas, algorithm = 'usearch', e = 0.01, bit = 40, length = .65, norm_bit = False):
"""
make and split a rbh network
"""
thresholds = [e, bit, length, norm_bit]
id2desc = get_descriptions(fastas)
# get [fasta, description, length] for ORF id
id2desc = self_compare(fastas, id... | def neto(fastas, algorithm = 'usearch', e = 0.01, bit = 40, length = .65, norm_bit = False):
"""
make and split a rbh network
"""
thresholds = [e, bit, length, norm_bit]
id2desc = get_descriptions(fastas)
# get [fasta, description, length] for ORF id
id2desc = self_compare(fastas, id... | [
"make",
"and",
"split",
"a",
"rbh",
"network"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L416-L445 | [
"def",
"neto",
"(",
"fastas",
",",
"algorithm",
"=",
"'usearch'",
",",
"e",
"=",
"0.01",
",",
"bit",
"=",
"40",
",",
"length",
"=",
".65",
",",
"norm_bit",
"=",
"False",
")",
":",
"thresholds",
"=",
"[",
"e",
",",
"bit",
",",
"length",
",",
"norm... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | network | make a rbh network for all pair-wise genome comparisons
- filter network based on normalized bit score (default, automatic) or specified e-value / bit score
- evaluate the scores for each genome pair compared
- build second network that is filtered so that clusters have only one ORF per genome
- evaluat... | ctbBio/neto.py | def network(thresholds, fastas, algorithm = 'usearch'):
"""
make a rbh network for all pair-wise genome comparisons
- filter network based on normalized bit score (default, automatic) or specified e-value / bit score
- evaluate the scores for each genome pair compared
- build second network that is ... | def network(thresholds, fastas, algorithm = 'usearch'):
"""
make a rbh network for all pair-wise genome comparisons
- filter network based on normalized bit score (default, automatic) or specified e-value / bit score
- evaluate the scores for each genome pair compared
- build second network that is ... | [
"make",
"a",
"rbh",
"network",
"for",
"all",
"pair",
"-",
"wise",
"genome",
"comparisons",
"-",
"filter",
"network",
"based",
"on",
"normalized",
"bit",
"score",
"(",
"default",
"automatic",
")",
"or",
"specified",
"e",
"-",
"value",
"/",
"bit",
"score",
... | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L447-L481 | [
"def",
"network",
"(",
"thresholds",
",",
"fastas",
",",
"algorithm",
"=",
"'usearch'",
")",
":",
"id2desc",
"=",
"get_descriptions",
"(",
"fastas",
")",
"# get [fasta, description, length] for ORF id",
"id2desc",
"=",
"self_compare",
"(",
"fastas",
",",
"id2desc",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | user_specific_data_directory | Returns the subdirectory in `userdata` which acts as the root of the
user-specific filesystem in Steam (aka all user-specific files are stored
under this directory) | pysteam/paths.py | def user_specific_data_directory(user_context):
"""Returns the subdirectory in `userdata` which acts as the root of the
user-specific filesystem in Steam (aka all user-specific files are stored
under this directory)"""
return os.path.join(
user_context.steam.userdata_directory,
user_context.user_id
) | def user_specific_data_directory(user_context):
"""Returns the subdirectory in `userdata` which acts as the root of the
user-specific filesystem in Steam (aka all user-specific files are stored
under this directory)"""
return os.path.join(
user_context.steam.userdata_directory,
user_context.user_id
) | [
"Returns",
"the",
"subdirectory",
"in",
"userdata",
"which",
"acts",
"as",
"the",
"root",
"of",
"the",
"user",
"-",
"specific",
"filesystem",
"in",
"Steam",
"(",
"aka",
"all",
"user",
"-",
"specific",
"files",
"are",
"stored",
"under",
"this",
"directory",
... | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/paths.py#L48-L55 | [
"def",
"user_specific_data_directory",
"(",
"user_context",
")",
":",
"return",
"os",
".",
"path",
".",
"join",
"(",
"user_context",
".",
"steam",
".",
"userdata_directory",
",",
"user_context",
".",
"user_id",
")"
] | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | IsoParser._init_data_map | OVERRIDDEN: Initialize required ISO-19115 data map with XPATHS and specialized functions | gis_metadata/iso_metadata_parser.py | def _init_data_map(self):
""" OVERRIDDEN: Initialize required ISO-19115 data map with XPATHS and specialized functions """
if self._data_map is not None:
return # Initiation happens once
# Parse and validate the ISO metadata root
if self._xml_tree is None:
iso... | def _init_data_map(self):
""" OVERRIDDEN: Initialize required ISO-19115 data map with XPATHS and specialized functions """
if self._data_map is not None:
return # Initiation happens once
# Parse and validate the ISO metadata root
if self._xml_tree is None:
iso... | [
"OVERRIDDEN",
":",
"Initialize",
"required",
"ISO",
"-",
"19115",
"data",
"map",
"with",
"XPATHS",
"and",
"specialized",
"functions"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L196-L353 | [
"def",
"_init_data_map",
"(",
"self",
")",
":",
"if",
"self",
".",
"_data_map",
"is",
"not",
"None",
":",
"return",
"# Initiation happens once",
"# Parse and validate the ISO metadata root",
"if",
"self",
".",
"_xml_tree",
"is",
"None",
":",
"iso_root",
"=",
"ISO_... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._parse_attribute_details | Concatenates a list of Attribute Details data structures parsed from a remote file | gis_metadata/iso_metadata_parser.py | def _parse_attribute_details(self, prop=ATTRIBUTES):
""" Concatenates a list of Attribute Details data structures parsed from a remote file """
parsed_attributes = self._parse_attribute_details_file(prop)
if parsed_attributes is None:
# If not in the (official) remote location, try ... | def _parse_attribute_details(self, prop=ATTRIBUTES):
""" Concatenates a list of Attribute Details data structures parsed from a remote file """
parsed_attributes = self._parse_attribute_details_file(prop)
if parsed_attributes is None:
# If not in the (official) remote location, try ... | [
"Concatenates",
"a",
"list",
"of",
"Attribute",
"Details",
"data",
"structures",
"parsed",
"from",
"a",
"remote",
"file"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L355-L367 | [
"def",
"_parse_attribute_details",
"(",
"self",
",",
"prop",
"=",
"ATTRIBUTES",
")",
":",
"parsed_attributes",
"=",
"self",
".",
"_parse_attribute_details_file",
"(",
"prop",
")",
"if",
"parsed_attributes",
"is",
"None",
":",
"# If not in the (official) remote location,... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._parse_attribute_details_file | Concatenates a list of Attribute Details data structures parsed from a remote file | gis_metadata/iso_metadata_parser.py | def _parse_attribute_details_file(self, prop=ATTRIBUTES):
""" Concatenates a list of Attribute Details data structures parsed from a remote file """
# Parse content from remote file URL, which may be stored in one of two places:
# Starting at: contentInfo/MD_FeatureCatalogueDescription/featu... | def _parse_attribute_details_file(self, prop=ATTRIBUTES):
""" Concatenates a list of Attribute Details data structures parsed from a remote file """
# Parse content from remote file URL, which may be stored in one of two places:
# Starting at: contentInfo/MD_FeatureCatalogueDescription/featu... | [
"Concatenates",
"a",
"list",
"of",
"Attribute",
"Details",
"data",
"structures",
"parsed",
"from",
"a",
"remote",
"file"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L369-L392 | [
"def",
"_parse_attribute_details_file",
"(",
"self",
",",
"prop",
"=",
"ATTRIBUTES",
")",
":",
"# Parse content from remote file URL, which may be stored in one of two places:",
"# Starting at: contentInfo/MD_FeatureCatalogueDescription/featureCatalogueCitation",
"# ATTRIBUTE: href",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._parse_digital_forms | Concatenates a list of Digital Form data structures parsed from the metadata | gis_metadata/iso_metadata_parser.py | def _parse_digital_forms(self, prop=DIGITAL_FORMS):
""" Concatenates a list of Digital Form data structures parsed from the metadata """
xpath_map = self._data_structures[prop]
# Parse base digital form fields: 'name', 'content', 'decompression', 'version', 'specification'
xpath_root =... | def _parse_digital_forms(self, prop=DIGITAL_FORMS):
""" Concatenates a list of Digital Form data structures parsed from the metadata """
xpath_map = self._data_structures[prop]
# Parse base digital form fields: 'name', 'content', 'decompression', 'version', 'specification'
xpath_root =... | [
"Concatenates",
"a",
"list",
"of",
"Digital",
"Form",
"data",
"structures",
"parsed",
"from",
"the",
"metadata"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L394-L451 | [
"def",
"_parse_digital_forms",
"(",
"self",
",",
"prop",
"=",
"DIGITAL_FORMS",
")",
":",
"xpath_map",
"=",
"self",
".",
"_data_structures",
"[",
"prop",
"]",
"# Parse base digital form fields: 'name', 'content', 'decompression', 'version', 'specification'",
"xpath_root",
"=",... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._parse_keywords | Parse type-specific keywords from the metadata: Theme or Place | gis_metadata/iso_metadata_parser.py | def _parse_keywords(self, prop):
""" Parse type-specific keywords from the metadata: Theme or Place """
keywords = []
if prop in KEYWORD_PROPS:
xpath_root = self._data_map['_keywords_root']
xpath_map = self._data_structures[prop]
xtype = xpath_map['keyword_... | def _parse_keywords(self, prop):
""" Parse type-specific keywords from the metadata: Theme or Place """
keywords = []
if prop in KEYWORD_PROPS:
xpath_root = self._data_map['_keywords_root']
xpath_map = self._data_structures[prop]
xtype = xpath_map['keyword_... | [
"Parse",
"type",
"-",
"specific",
"keywords",
"from",
"the",
"metadata",
":",
"Theme",
"or",
"Place"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L453-L470 | [
"def",
"_parse_keywords",
"(",
"self",
",",
"prop",
")",
":",
"keywords",
"=",
"[",
"]",
"if",
"prop",
"in",
"KEYWORD_PROPS",
":",
"xpath_root",
"=",
"self",
".",
"_data_map",
"[",
"'_keywords_root'",
"]",
"xpath_map",
"=",
"self",
".",
"_data_structures",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._parse_raster_info | Collapses multiple dimensions into a single raster_info complex struct | gis_metadata/iso_metadata_parser.py | def _parse_raster_info(self, prop=RASTER_INFO):
""" Collapses multiple dimensions into a single raster_info complex struct """
raster_info = {}.fromkeys(_iso_definitions[prop], u'')
# Ensure conversion of lists to newlines is in place
raster_info['dimensions'] = get_default_for_complex... | def _parse_raster_info(self, prop=RASTER_INFO):
""" Collapses multiple dimensions into a single raster_info complex struct """
raster_info = {}.fromkeys(_iso_definitions[prop], u'')
# Ensure conversion of lists to newlines is in place
raster_info['dimensions'] = get_default_for_complex... | [
"Collapses",
"multiple",
"dimensions",
"into",
"a",
"single",
"raster_info",
"complex",
"struct"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L472-L502 | [
"def",
"_parse_raster_info",
"(",
"self",
",",
"prop",
"=",
"RASTER_INFO",
")",
":",
"raster_info",
"=",
"{",
"}",
".",
"fromkeys",
"(",
"_iso_definitions",
"[",
"prop",
"]",
",",
"u''",
")",
"# Ensure conversion of lists to newlines is in place",
"raster_info",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._update_attribute_details | Update operation for ISO Attribute Details metadata: write to "MD_Metadata/featureType" | gis_metadata/iso_metadata_parser.py | def _update_attribute_details(self, **update_props):
""" Update operation for ISO Attribute Details metadata: write to "MD_Metadata/featureType" """
tree_to_update = update_props['tree_to_update']
xpath = self._data_map['_attr_citation']
# Cannot write to remote file: remove the featur... | def _update_attribute_details(self, **update_props):
""" Update operation for ISO Attribute Details metadata: write to "MD_Metadata/featureType" """
tree_to_update = update_props['tree_to_update']
xpath = self._data_map['_attr_citation']
# Cannot write to remote file: remove the featur... | [
"Update",
"operation",
"for",
"ISO",
"Attribute",
"Details",
"metadata",
":",
"write",
"to",
"MD_Metadata",
"/",
"featureType"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L504-L515 | [
"def",
"_update_attribute_details",
"(",
"self",
",",
"*",
"*",
"update_props",
")",
":",
"tree_to_update",
"=",
"update_props",
"[",
"'tree_to_update'",
"]",
"xpath",
"=",
"self",
".",
"_data_map",
"[",
"'_attr_citation'",
"]",
"# Cannot write to remote file: remove ... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._update_digital_forms | Update operation for ISO Digital Forms metadata
:see: gis_metadata.utils._complex_definitions[DIGITAL_FORMS] | gis_metadata/iso_metadata_parser.py | def _update_digital_forms(self, **update_props):
"""
Update operation for ISO Digital Forms metadata
:see: gis_metadata.utils._complex_definitions[DIGITAL_FORMS]
"""
digital_forms = wrap_value(update_props['values'])
# Update all Digital Form properties: distributionFor... | def _update_digital_forms(self, **update_props):
"""
Update operation for ISO Digital Forms metadata
:see: gis_metadata.utils._complex_definitions[DIGITAL_FORMS]
"""
digital_forms = wrap_value(update_props['values'])
# Update all Digital Form properties: distributionFor... | [
"Update",
"operation",
"for",
"ISO",
"Digital",
"Forms",
"metadata",
":",
"see",
":",
"gis_metadata",
".",
"utils",
".",
"_complex_definitions",
"[",
"DIGITAL_FORMS",
"]"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L539-L590 | [
"def",
"_update_digital_forms",
"(",
"self",
",",
"*",
"*",
"update_props",
")",
":",
"digital_forms",
"=",
"wrap_value",
"(",
"update_props",
"[",
"'values'",
"]",
")",
"# Update all Digital Form properties: distributionFormat*",
"xpath_map",
"=",
"self",
".",
"_data... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._update_keywords | Update operation for ISO type-specific Keywords metadata: Theme or Place | gis_metadata/iso_metadata_parser.py | def _update_keywords(self, **update_props):
""" Update operation for ISO type-specific Keywords metadata: Theme or Place """
tree_to_update = update_props['tree_to_update']
prop = update_props['prop']
values = update_props['values']
keywords = []
if prop in KEYWORD_PRO... | def _update_keywords(self, **update_props):
""" Update operation for ISO type-specific Keywords metadata: Theme or Place """
tree_to_update = update_props['tree_to_update']
prop = update_props['prop']
values = update_props['values']
keywords = []
if prop in KEYWORD_PRO... | [
"Update",
"operation",
"for",
"ISO",
"type",
"-",
"specific",
"Keywords",
"metadata",
":",
"Theme",
"or",
"Place"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L592-L620 | [
"def",
"_update_keywords",
"(",
"self",
",",
"*",
"*",
"update_props",
")",
":",
"tree_to_update",
"=",
"update_props",
"[",
"'tree_to_update'",
"]",
"prop",
"=",
"update_props",
"[",
"'prop'",
"]",
"values",
"=",
"update_props",
"[",
"'values'",
"]",
"keyword... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._update_raster_info | Derives multiple dimensions from a single raster_info complex struct | gis_metadata/iso_metadata_parser.py | def _update_raster_info(self, **update_props):
""" Derives multiple dimensions from a single raster_info complex struct """
tree_to_update = update_props['tree_to_update']
prop = update_props['prop']
values = update_props.pop('values')
# Update number of dimensions at raster_in... | def _update_raster_info(self, **update_props):
""" Derives multiple dimensions from a single raster_info complex struct """
tree_to_update = update_props['tree_to_update']
prop = update_props['prop']
values = update_props.pop('values')
# Update number of dimensions at raster_in... | [
"Derives",
"multiple",
"dimensions",
"from",
"a",
"single",
"raster_info",
"complex",
"struct"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L622-L666 | [
"def",
"_update_raster_info",
"(",
"self",
",",
"*",
"*",
"update_props",
")",
":",
"tree_to_update",
"=",
"update_props",
"[",
"'tree_to_update'",
"]",
"prop",
"=",
"update_props",
"[",
"'prop'",
"]",
"values",
"=",
"update_props",
".",
"pop",
"(",
"'values'"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser.update | OVERRIDDEN: Prevents writing multiple CharacterStrings per XPATH property | gis_metadata/iso_metadata_parser.py | def update(self, use_template=False, **metadata_defaults):
""" OVERRIDDEN: Prevents writing multiple CharacterStrings per XPATH property """
self.validate()
tree_to_update = self._xml_tree if not use_template else self._get_template(**metadata_defaults)
supported_props = self._metadata... | def update(self, use_template=False, **metadata_defaults):
""" OVERRIDDEN: Prevents writing multiple CharacterStrings per XPATH property """
self.validate()
tree_to_update = self._xml_tree if not use_template else self._get_template(**metadata_defaults)
supported_props = self._metadata... | [
"OVERRIDDEN",
":",
"Prevents",
"writing",
"multiple",
"CharacterStrings",
"per",
"XPATH",
"property"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L668-L689 | [
"def",
"update",
"(",
"self",
",",
"use_template",
"=",
"False",
",",
"*",
"*",
"metadata_defaults",
")",
":",
"self",
".",
"validate",
"(",
")",
"tree_to_update",
"=",
"self",
".",
"_xml_tree",
"if",
"not",
"use_template",
"else",
"self",
".",
"_get_templ... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | IsoParser._trim_xpath | Removes primitive type tags from an XPATH | gis_metadata/iso_metadata_parser.py | def _trim_xpath(self, xpath, prop):
""" Removes primitive type tags from an XPATH """
xroot = self._get_xroot_for(prop)
if xroot is None and isinstance(xpath, string_types):
xtags = xpath.split(XPATH_DELIM)
if xtags[-1] in _iso_tag_primitives:
xroot = X... | def _trim_xpath(self, xpath, prop):
""" Removes primitive type tags from an XPATH """
xroot = self._get_xroot_for(prop)
if xroot is None and isinstance(xpath, string_types):
xtags = xpath.split(XPATH_DELIM)
if xtags[-1] in _iso_tag_primitives:
xroot = X... | [
"Removes",
"primitive",
"type",
"tags",
"from",
"an",
"XPATH"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L691-L702 | [
"def",
"_trim_xpath",
"(",
"self",
",",
"xpath",
",",
"prop",
")",
":",
"xroot",
"=",
"self",
".",
"_get_xroot_for",
"(",
"prop",
")",
"if",
"xroot",
"is",
"None",
"and",
"isinstance",
"(",
"xpath",
",",
"string_types",
")",
":",
"xtags",
"=",
"xpath",... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | shortcut_app_id | Generates the app id for a given shortcut. Steam uses app ids as a unique
identifier for games, but since shortcuts dont have a canonical serverside
representation they need to be generated on the fly. The important part
about this function is that it will generate the same app id as Steam does
for a given shor... | pysteam/shortcuts.py | def shortcut_app_id(shortcut):
"""
Generates the app id for a given shortcut. Steam uses app ids as a unique
identifier for games, but since shortcuts dont have a canonical serverside
representation they need to be generated on the fly. The important part
about this function is that it will generate the same ... | def shortcut_app_id(shortcut):
"""
Generates the app id for a given shortcut. Steam uses app ids as a unique
identifier for games, but since shortcuts dont have a canonical serverside
representation they need to be generated on the fly. The important part
about this function is that it will generate the same ... | [
"Generates",
"the",
"app",
"id",
"for",
"a",
"given",
"shortcut",
".",
"Steam",
"uses",
"app",
"ids",
"as",
"a",
"unique",
"identifier",
"for",
"games",
"but",
"since",
"shortcuts",
"dont",
"have",
"a",
"canonical",
"serverside",
"representation",
"they",
"n... | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/shortcuts.py#L9-L21 | [
"def",
"shortcut_app_id",
"(",
"shortcut",
")",
":",
"algorithm",
"=",
"Crc",
"(",
"width",
"=",
"32",
",",
"poly",
"=",
"0x04C11DB7",
",",
"reflect_in",
"=",
"True",
",",
"xor_in",
"=",
"0xffffffff",
",",
"reflect_out",
"=",
"True",
",",
"xor_out",
"=",... | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | VCS._config | Execute git config. | bootstrap_py/vcs.py | def _config(self):
"""Execute git config."""
cfg_wr = self.repo.config_writer()
cfg_wr.add_section('user')
cfg_wr.set_value('user', 'name', self.metadata.author)
cfg_wr.set_value('user', 'email', self.metadata.email)
cfg_wr.release() | def _config(self):
"""Execute git config."""
cfg_wr = self.repo.config_writer()
cfg_wr.add_section('user')
cfg_wr.set_value('user', 'name', self.metadata.author)
cfg_wr.set_value('user', 'email', self.metadata.email)
cfg_wr.release() | [
"Execute",
"git",
"config",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/vcs.py#L35-L41 | [
"def",
"_config",
"(",
"self",
")",
":",
"cfg_wr",
"=",
"self",
".",
"repo",
".",
"config_writer",
"(",
")",
"cfg_wr",
".",
"add_section",
"(",
"'user'",
")",
"cfg_wr",
".",
"set_value",
"(",
"'user'",
",",
"'name'",
",",
"self",
".",
"metadata",
".",
... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | VCS._remote_add | Execute git remote add. | bootstrap_py/vcs.py | def _remote_add(self):
"""Execute git remote add."""
self.repo.create_remote(
'origin',
'git@github.com:{username}/{repo}.git'.format(
username=self.metadata.username,
repo=self.metadata.name)) | def _remote_add(self):
"""Execute git remote add."""
self.repo.create_remote(
'origin',
'git@github.com:{username}/{repo}.git'.format(
username=self.metadata.username,
repo=self.metadata.name)) | [
"Execute",
"git",
"remote",
"add",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/vcs.py#L47-L53 | [
"def",
"_remote_add",
"(",
"self",
")",
":",
"self",
".",
"repo",
".",
"create_remote",
"(",
"'origin'",
",",
"'git@github.com:{username}/{repo}.git'",
".",
"format",
"(",
"username",
"=",
"self",
".",
"metadata",
".",
"username",
",",
"repo",
"=",
"self",
"... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | BaseScript.start | Starts execution of the script | basescript/basescript.py | def start(self):
'''
Starts execution of the script
'''
# invoke the appropriate sub-command as requested from command-line
try:
self.args.func()
except SystemExit as e:
if e.code != 0:
raise
except KeyboardInterrupt:
... | def start(self):
'''
Starts execution of the script
'''
# invoke the appropriate sub-command as requested from command-line
try:
self.args.func()
except SystemExit as e:
if e.code != 0:
raise
except KeyboardInterrupt:
... | [
"Starts",
"execution",
"of",
"the",
"script"
] | deep-compute/basescript | python | https://github.com/deep-compute/basescript/blob/f7233963c5291530fcb2444a7f45b556e6407b90/basescript/basescript.py#L67-L87 | [
"def",
"start",
"(",
"self",
")",
":",
"# invoke the appropriate sub-command as requested from command-line",
"try",
":",
"self",
".",
"args",
".",
"func",
"(",
")",
"except",
"SystemExit",
"as",
"e",
":",
"if",
"e",
".",
"code",
"!=",
"0",
":",
"raise",
"ex... | f7233963c5291530fcb2444a7f45b556e6407b90 |
train | BaseScript.define_baseargs | Define basic command-line arguments required by the script.
@parser is a parser object created using the `argparse` module.
returns: None | basescript/basescript.py | def define_baseargs(self, parser):
'''
Define basic command-line arguments required by the script.
@parser is a parser object created using the `argparse` module.
returns: None
'''
parser.add_argument('--name', default=sys.argv[0],
help='Name to identify this ... | def define_baseargs(self, parser):
'''
Define basic command-line arguments required by the script.
@parser is a parser object created using the `argparse` module.
returns: None
'''
parser.add_argument('--name', default=sys.argv[0],
help='Name to identify this ... | [
"Define",
"basic",
"command",
"-",
"line",
"arguments",
"required",
"by",
"the",
"script",
"."
] | deep-compute/basescript | python | https://github.com/deep-compute/basescript/blob/f7233963c5291530fcb2444a7f45b556e6407b90/basescript/basescript.py#L123-L151 | [
"def",
"define_baseargs",
"(",
"self",
",",
"parser",
")",
":",
"parser",
".",
"add_argument",
"(",
"'--name'",
",",
"default",
"=",
"sys",
".",
"argv",
"[",
"0",
"]",
",",
"help",
"=",
"'Name to identify this instance'",
")",
"parser",
".",
"add_argument",
... | f7233963c5291530fcb2444a7f45b556e6407b90 |
train | SourceCoder.cleanup_payload | Basically, turns payload that looks like ' \\n ' to ''. In the
calling function, if this function returns '' no object is added
for that payload. | uno/parser/source_coder.py | def cleanup_payload(self, payload):
"""
Basically, turns payload that looks like ' \\n ' to ''. In the
calling function, if this function returns '' no object is added
for that payload.
"""
p = payload.replace('\n', '')
p = p.rstrip()
p = p.lstrip()
... | def cleanup_payload(self, payload):
"""
Basically, turns payload that looks like ' \\n ' to ''. In the
calling function, if this function returns '' no object is added
for that payload.
"""
p = payload.replace('\n', '')
p = p.rstrip()
p = p.lstrip()
... | [
"Basically",
"turns",
"payload",
"that",
"looks",
"like",
"\\\\",
"n",
"to",
".",
"In",
"the",
"calling",
"function",
"if",
"this",
"function",
"returns",
"no",
"object",
"is",
"added",
"for",
"that",
"payload",
"."
] | elbow-jason/Uno-deprecated | python | https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/parser/source_coder.py#L73-L82 | [
"def",
"cleanup_payload",
"(",
"self",
",",
"payload",
")",
":",
"p",
"=",
"payload",
".",
"replace",
"(",
"'\\n'",
",",
"''",
")",
"p",
"=",
"p",
".",
"rstrip",
"(",
")",
"p",
"=",
"p",
".",
"lstrip",
"(",
")",
"return",
"p"
] | 4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4 |
train | format_xpaths | :return: a copy of xpath_map, but with XPATHs formatted with ordered or keyword values | gis_metadata/utils.py | def format_xpaths(xpath_map, *args, **kwargs):
""" :return: a copy of xpath_map, but with XPATHs formatted with ordered or keyword values """
formatted = {}.fromkeys(xpath_map)
for key, xpath in iteritems(xpath_map):
formatted[key] = xpath.format(*args, **kwargs)
return formatted | def format_xpaths(xpath_map, *args, **kwargs):
""" :return: a copy of xpath_map, but with XPATHs formatted with ordered or keyword values """
formatted = {}.fromkeys(xpath_map)
for key, xpath in iteritems(xpath_map):
formatted[key] = xpath.format(*args, **kwargs)
return formatted | [
":",
"return",
":",
"a",
"copy",
"of",
"xpath_map",
"but",
"with",
"XPATHs",
"formatted",
"with",
"ordered",
"or",
"keyword",
"values"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L162-L170 | [
"def",
"format_xpaths",
"(",
"xpath_map",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"formatted",
"=",
"{",
"}",
".",
"fromkeys",
"(",
"xpath_map",
")",
"for",
"key",
",",
"xpath",
"in",
"iteritems",
"(",
"xpath_map",
")",
":",
"formatted",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | get_xpath_root | :return: the base of an XPATH: the part preceding any format keys or attribute references | gis_metadata/utils.py | def get_xpath_root(xpath):
""" :return: the base of an XPATH: the part preceding any format keys or attribute references """
if xpath:
if xpath.startswith('@'):
xpath = ''
else:
index = xpath.find('/@' if '@' in xpath else '/{')
xpath = xpath[:index] if index... | def get_xpath_root(xpath):
""" :return: the base of an XPATH: the part preceding any format keys or attribute references """
if xpath:
if xpath.startswith('@'):
xpath = ''
else:
index = xpath.find('/@' if '@' in xpath else '/{')
xpath = xpath[:index] if index... | [
":",
"return",
":",
"the",
"base",
"of",
"an",
"XPATH",
":",
"the",
"part",
"preceding",
"any",
"format",
"keys",
"or",
"attribute",
"references"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L188-L198 | [
"def",
"get_xpath_root",
"(",
"xpath",
")",
":",
"if",
"xpath",
":",
"if",
"xpath",
".",
"startswith",
"(",
"'@'",
")",
":",
"xpath",
"=",
"''",
"else",
":",
"index",
"=",
"xpath",
".",
"find",
"(",
"'/@'",
"if",
"'@'",
"in",
"xpath",
"else",
"'/{'... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | get_xpath_branch | :return: the relative part of an XPATH: that which extends past the root provided | gis_metadata/utils.py | def get_xpath_branch(xroot, xpath):
""" :return: the relative part of an XPATH: that which extends past the root provided """
if xroot and xpath and xpath.startswith(xroot):
xpath = xpath[len(xroot):]
xpath = xpath.lstrip(XPATH_DELIM)
return xpath | def get_xpath_branch(xroot, xpath):
""" :return: the relative part of an XPATH: that which extends past the root provided """
if xroot and xpath and xpath.startswith(xroot):
xpath = xpath[len(xroot):]
xpath = xpath.lstrip(XPATH_DELIM)
return xpath | [
":",
"return",
":",
"the",
"relative",
"part",
"of",
"an",
"XPATH",
":",
"that",
"which",
"extends",
"past",
"the",
"root",
"provided"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L201-L208 | [
"def",
"get_xpath_branch",
"(",
"xroot",
",",
"xpath",
")",
":",
"if",
"xroot",
"and",
"xpath",
"and",
"xpath",
".",
"startswith",
"(",
"xroot",
")",
":",
"xpath",
"=",
"xpath",
"[",
"len",
"(",
"xroot",
")",
":",
"]",
"xpath",
"=",
"xpath",
".",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | get_xpath_tuple | :return: a tuple with the base of an XPATH followed by any format key or attribute reference | gis_metadata/utils.py | def get_xpath_tuple(xpath):
""" :return: a tuple with the base of an XPATH followed by any format key or attribute reference """
xroot = get_xpath_root(xpath)
xattr = None
if xroot != xpath:
xattr = get_xpath_branch(xroot, xpath).strip('@')
return (xroot, xattr) | def get_xpath_tuple(xpath):
""" :return: a tuple with the base of an XPATH followed by any format key or attribute reference """
xroot = get_xpath_root(xpath)
xattr = None
if xroot != xpath:
xattr = get_xpath_branch(xroot, xpath).strip('@')
return (xroot, xattr) | [
":",
"return",
":",
"a",
"tuple",
"with",
"the",
"base",
"of",
"an",
"XPATH",
"followed",
"by",
"any",
"format",
"key",
"or",
"attribute",
"reference"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L211-L220 | [
"def",
"get_xpath_tuple",
"(",
"xpath",
")",
":",
"xroot",
"=",
"get_xpath_root",
"(",
"xpath",
")",
"xattr",
"=",
"None",
"if",
"xroot",
"!=",
"xpath",
":",
"xattr",
"=",
"get_xpath_branch",
"(",
"xroot",
",",
"xpath",
")",
".",
"strip",
"(",
"'@'",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | get_default_for | Ensures complex property types have the correct default values | gis_metadata/utils.py | def get_default_for(prop, value):
""" Ensures complex property types have the correct default values """
prop = prop.strip('_') # Handle alternate props (leading underscores)
val = reduce_value(value) # Filtering of value happens here
if prop in _COMPLEX_LISTS:
return wrap_value(val)
... | def get_default_for(prop, value):
""" Ensures complex property types have the correct default values """
prop = prop.strip('_') # Handle alternate props (leading underscores)
val = reduce_value(value) # Filtering of value happens here
if prop in _COMPLEX_LISTS:
return wrap_value(val)
... | [
"Ensures",
"complex",
"property",
"types",
"have",
"the",
"correct",
"default",
"values"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L223-L234 | [
"def",
"get_default_for",
"(",
"prop",
",",
"value",
")",
":",
"prop",
"=",
"prop",
".",
"strip",
"(",
"'_'",
")",
"# Handle alternate props (leading underscores)",
"val",
"=",
"reduce_value",
"(",
"value",
")",
"# Filtering of value happens here",
"if",
"prop",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | has_property | Parse xpath for any attribute reference "path/@attr" and check for root and presence of attribute.
:return: True if xpath is present in the element along with any attribute referenced, otherwise False | gis_metadata/utils.py | def has_property(elem_to_parse, xpath):
"""
Parse xpath for any attribute reference "path/@attr" and check for root and presence of attribute.
:return: True if xpath is present in the element along with any attribute referenced, otherwise False
"""
xroot, attr = get_xpath_tuple(xpath)
if not x... | def has_property(elem_to_parse, xpath):
"""
Parse xpath for any attribute reference "path/@attr" and check for root and presence of attribute.
:return: True if xpath is present in the element along with any attribute referenced, otherwise False
"""
xroot, attr = get_xpath_tuple(xpath)
if not x... | [
"Parse",
"xpath",
"for",
"any",
"attribute",
"reference",
"path",
"/"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L262-L275 | [
"def",
"has_property",
"(",
"elem_to_parse",
",",
"xpath",
")",
":",
"xroot",
",",
"attr",
"=",
"get_xpath_tuple",
"(",
"xpath",
")",
"if",
"not",
"xroot",
"and",
"not",
"attr",
":",
"return",
"False",
"elif",
"not",
"attr",
":",
"return",
"bool",
"(",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | parse_complex | Creates and returns a Dictionary data structure parsed from the metadata.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: the XPATH location of the structure inside the parent element
:param xpath_map: a dict of XPATHs corresponding to a complex definition
... | gis_metadata/utils.py | def parse_complex(tree_to_parse, xpath_root, xpath_map, complex_key):
"""
Creates and returns a Dictionary data structure parsed from the metadata.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: the XPATH location of the structure inside the parent eleme... | def parse_complex(tree_to_parse, xpath_root, xpath_map, complex_key):
"""
Creates and returns a Dictionary data structure parsed from the metadata.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: the XPATH location of the structure inside the parent eleme... | [
"Creates",
"and",
"returns",
"a",
"Dictionary",
"data",
"structure",
"parsed",
"from",
"the",
"metadata",
".",
":",
"param",
"tree_to_parse",
":",
"the",
"XML",
"tree",
"compatible",
"with",
"element_utils",
"to",
"be",
"parsed",
":",
"param",
"xpath_root",
":... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L278-L296 | [
"def",
"parse_complex",
"(",
"tree_to_parse",
",",
"xpath_root",
",",
"xpath_map",
",",
"complex_key",
")",
":",
"complex_struct",
"=",
"{",
"}",
"for",
"prop",
"in",
"_complex_definitions",
".",
"get",
"(",
"complex_key",
",",
"xpath_map",
")",
":",
"# Normal... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | parse_complex_list | Creates and returns a list of Dictionary data structures parsed from the metadata.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: the XPATH location of each structure inside the parent element
:param xpath_map: a dict of XPATHs corresponding to a complex def... | gis_metadata/utils.py | def parse_complex_list(tree_to_parse, xpath_root, xpath_map, complex_key):
"""
Creates and returns a list of Dictionary data structures parsed from the metadata.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: the XPATH location of each structure inside t... | def parse_complex_list(tree_to_parse, xpath_root, xpath_map, complex_key):
"""
Creates and returns a list of Dictionary data structures parsed from the metadata.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: the XPATH location of each structure inside t... | [
"Creates",
"and",
"returns",
"a",
"list",
"of",
"Dictionary",
"data",
"structures",
"parsed",
"from",
"the",
"metadata",
".",
":",
"param",
"tree_to_parse",
":",
"the",
"XML",
"tree",
"compatible",
"with",
"element_utils",
"to",
"be",
"parsed",
":",
"param",
... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L299-L315 | [
"def",
"parse_complex_list",
"(",
"tree_to_parse",
",",
"xpath_root",
",",
"xpath_map",
",",
"complex_key",
")",
":",
"complex_list",
"=",
"[",
"]",
"for",
"element",
"in",
"get_elements",
"(",
"tree_to_parse",
",",
"xpath_root",
")",
":",
"complex_struct",
"=",... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | parse_dates | Creates and returns a Dates Dictionary data structure given the parameters provided
:param tree_to_parse: the XML tree from which to construct the Dates data structure
:param xpath_map: a map containing the following type-specific XPATHs:
multiple, range, range_begin, range_end, and single | gis_metadata/utils.py | def parse_dates(tree_to_parse, xpath_map):
"""
Creates and returns a Dates Dictionary data structure given the parameters provided
:param tree_to_parse: the XML tree from which to construct the Dates data structure
:param xpath_map: a map containing the following type-specific XPATHs:
multiple, ... | def parse_dates(tree_to_parse, xpath_map):
"""
Creates and returns a Dates Dictionary data structure given the parameters provided
:param tree_to_parse: the XML tree from which to construct the Dates data structure
:param xpath_map: a map containing the following type-specific XPATHs:
multiple, ... | [
"Creates",
"and",
"returns",
"a",
"Dates",
"Dictionary",
"data",
"structure",
"given",
"the",
"parameters",
"provided",
":",
"param",
"tree_to_parse",
":",
"the",
"XML",
"tree",
"from",
"which",
"to",
"construct",
"the",
"Dates",
"data",
"structure",
":",
"par... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L318-L351 | [
"def",
"parse_dates",
"(",
"tree_to_parse",
",",
"xpath_map",
")",
":",
"# Determine dates to query based on metadata elements",
"values",
"=",
"wrap_value",
"(",
"parse_property",
"(",
"tree_to_parse",
",",
"None",
",",
"xpath_map",
",",
"DATE_TYPE_SINGLE",
")",
")",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | parse_property | Defines the default parsing behavior for metadata values.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: used to determine the relative XPATH location within the parent element
:param xpath_map: a dict of XPATHs that may contain alternate locations for a pro... | gis_metadata/utils.py | def parse_property(tree_to_parse, xpath_root, xpath_map, prop):
"""
Defines the default parsing behavior for metadata values.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: used to determine the relative XPATH location within the parent element
:para... | def parse_property(tree_to_parse, xpath_root, xpath_map, prop):
"""
Defines the default parsing behavior for metadata values.
:param tree_to_parse: the XML tree compatible with element_utils to be parsed
:param xpath_root: used to determine the relative XPATH location within the parent element
:para... | [
"Defines",
"the",
"default",
"parsing",
"behavior",
"for",
"metadata",
"values",
".",
":",
"param",
"tree_to_parse",
":",
"the",
"XML",
"tree",
"compatible",
"with",
"element_utils",
"to",
"be",
"parsed",
":",
"param",
"xpath_root",
":",
"used",
"to",
"determi... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L354-L389 | [
"def",
"parse_property",
"(",
"tree_to_parse",
",",
"xpath_root",
",",
"xpath_map",
",",
"prop",
")",
":",
"xpath",
"=",
"xpath_map",
"[",
"prop",
"]",
"if",
"isinstance",
"(",
"xpath",
",",
"ParserProperty",
")",
":",
"if",
"xpath",
".",
"xpath",
"is",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | update_property | Either update the tree the default way, or call the custom updater
Default Way: Existing values in the tree are overwritten. If xpaths contains a single path,
then each value is written to the tree at that path. If xpaths contains a list of xpaths,
then the values corresponding to each xpath index are writ... | gis_metadata/utils.py | def update_property(tree_to_update, xpath_root, xpaths, prop, values, supported=None):
"""
Either update the tree the default way, or call the custom updater
Default Way: Existing values in the tree are overwritten. If xpaths contains a single path,
then each value is written to the tree at that path. ... | def update_property(tree_to_update, xpath_root, xpaths, prop, values, supported=None):
"""
Either update the tree the default way, or call the custom updater
Default Way: Existing values in the tree are overwritten. If xpaths contains a single path,
then each value is written to the tree at that path. ... | [
"Either",
"update",
"the",
"tree",
"the",
"default",
"way",
"or",
"call",
"the",
"custom",
"updater"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L392-L423 | [
"def",
"update_property",
"(",
"tree_to_update",
",",
"xpath_root",
",",
"xpaths",
",",
"prop",
",",
"values",
",",
"supported",
"=",
"None",
")",
":",
"if",
"supported",
"and",
"prop",
".",
"startswith",
"(",
"'_'",
")",
"and",
"prop",
".",
"strip",
"("... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | _update_property | Default update operation for a single parser property. If xpaths contains one xpath,
then one element per value will be inserted at that location in the tree_to_update;
otherwise, the number of values must match the number of xpaths. | gis_metadata/utils.py | def _update_property(tree_to_update, xpath_root, xpaths, values):
"""
Default update operation for a single parser property. If xpaths contains one xpath,
then one element per value will be inserted at that location in the tree_to_update;
otherwise, the number of values must match the number of xpaths.
... | def _update_property(tree_to_update, xpath_root, xpaths, values):
"""
Default update operation for a single parser property. If xpaths contains one xpath,
then one element per value will be inserted at that location in the tree_to_update;
otherwise, the number of values must match the number of xpaths.
... | [
"Default",
"update",
"operation",
"for",
"a",
"single",
"parser",
"property",
".",
"If",
"xpaths",
"contains",
"one",
"xpath",
"then",
"one",
"element",
"per",
"value",
"will",
"be",
"inserted",
"at",
"that",
"location",
"in",
"the",
"tree_to_update",
";",
"... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L426-L486 | [
"def",
"_update_property",
"(",
"tree_to_update",
",",
"xpath_root",
",",
"xpaths",
",",
"values",
")",
":",
"# Inner function to update a specific XPATH with the values provided",
"def",
"update_element",
"(",
"elem",
",",
"idx",
",",
"root",
",",
"path",
",",
"vals"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | update_complex | Updates and returns the updated complex Element parsed from tree_to_update.
:param tree_to_update: the XML tree compatible with element_utils to be updated
:param xpath_root: the XPATH location of the root of the complex Element
:param xpath_map: a Dictionary of XPATHs corresponding to the complex structure... | gis_metadata/utils.py | def update_complex(tree_to_update, xpath_root, xpath_map, prop, values):
"""
Updates and returns the updated complex Element parsed from tree_to_update.
:param tree_to_update: the XML tree compatible with element_utils to be updated
:param xpath_root: the XPATH location of the root of the complex Elemen... | def update_complex(tree_to_update, xpath_root, xpath_map, prop, values):
"""
Updates and returns the updated complex Element parsed from tree_to_update.
:param tree_to_update: the XML tree compatible with element_utils to be updated
:param xpath_root: the XPATH location of the root of the complex Elemen... | [
"Updates",
"and",
"returns",
"the",
"updated",
"complex",
"Element",
"parsed",
"from",
"tree_to_update",
".",
":",
"param",
"tree_to_update",
":",
"the",
"XML",
"tree",
"compatible",
"with",
"element_utils",
"to",
"be",
"updated",
":",
"param",
"xpath_root",
":"... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L489-L513 | [
"def",
"update_complex",
"(",
"tree_to_update",
",",
"xpath_root",
",",
"xpath_map",
",",
"prop",
",",
"values",
")",
":",
"remove_element",
"(",
"tree_to_update",
",",
"xpath_root",
",",
"True",
")",
"values",
"=",
"reduce_value",
"(",
"values",
",",
"{",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | update_complex_list | Updates and returns the list of updated complex Elements parsed from tree_to_update.
:param tree_to_update: the XML tree compatible with element_utils to be updated
:param xpath_root: the XPATH location of each complex Element
:param xpath_map: a Dictionary of XPATHs corresponding to the complex structure d... | gis_metadata/utils.py | def update_complex_list(tree_to_update, xpath_root, xpath_map, prop, values):
"""
Updates and returns the list of updated complex Elements parsed from tree_to_update.
:param tree_to_update: the XML tree compatible with element_utils to be updated
:param xpath_root: the XPATH location of each complex Ele... | def update_complex_list(tree_to_update, xpath_root, xpath_map, prop, values):
"""
Updates and returns the list of updated complex Elements parsed from tree_to_update.
:param tree_to_update: the XML tree compatible with element_utils to be updated
:param xpath_root: the XPATH location of each complex Ele... | [
"Updates",
"and",
"returns",
"the",
"list",
"of",
"updated",
"complex",
"Elements",
"parsed",
"from",
"tree_to_update",
".",
":",
"param",
"tree_to_update",
":",
"the",
"XML",
"tree",
"compatible",
"with",
"element_utils",
"to",
"be",
"updated",
":",
"param",
... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L516-L544 | [
"def",
"update_complex_list",
"(",
"tree_to_update",
",",
"xpath_root",
",",
"xpath_map",
",",
"prop",
",",
"values",
")",
":",
"complex_list",
"=",
"[",
"]",
"remove_element",
"(",
"tree_to_update",
",",
"xpath_root",
",",
"True",
")",
"if",
"not",
"values",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | validate_any | Validates any metadata property, complex or simple (string or array) | gis_metadata/utils.py | def validate_any(prop, value, xpath_map=None):
""" Validates any metadata property, complex or simple (string or array) """
if value is not None:
if prop in (ATTRIBUTES, CONTACTS, DIGITAL_FORMS):
validate_complex_list(prop, value, xpath_map)
elif prop in (BOUNDING_BOX, LARGER_WORKS... | def validate_any(prop, value, xpath_map=None):
""" Validates any metadata property, complex or simple (string or array) """
if value is not None:
if prop in (ATTRIBUTES, CONTACTS, DIGITAL_FORMS):
validate_complex_list(prop, value, xpath_map)
elif prop in (BOUNDING_BOX, LARGER_WORKS... | [
"Validates",
"any",
"metadata",
"property",
"complex",
"or",
"simple",
"(",
"string",
"or",
"array",
")"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L547-L569 | [
"def",
"validate_any",
"(",
"prop",
",",
"value",
",",
"xpath_map",
"=",
"None",
")",
":",
"if",
"value",
"is",
"not",
"None",
":",
"if",
"prop",
"in",
"(",
"ATTRIBUTES",
",",
"CONTACTS",
",",
"DIGITAL_FORMS",
")",
":",
"validate_complex_list",
"(",
"pro... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | validate_complex | Default validation for single complex data structure | gis_metadata/utils.py | def validate_complex(prop, value, xpath_map=None):
""" Default validation for single complex data structure """
if value is not None:
validate_type(prop, value, dict)
if prop in _complex_definitions:
complex_keys = _complex_definitions[prop]
else:
complex_keys =... | def validate_complex(prop, value, xpath_map=None):
""" Default validation for single complex data structure """
if value is not None:
validate_type(prop, value, dict)
if prop in _complex_definitions:
complex_keys = _complex_definitions[prop]
else:
complex_keys =... | [
"Default",
"validation",
"for",
"single",
"complex",
"data",
"structure"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L572-L589 | [
"def",
"validate_complex",
"(",
"prop",
",",
"value",
",",
"xpath_map",
"=",
"None",
")",
":",
"if",
"value",
"is",
"not",
"None",
":",
"validate_type",
"(",
"prop",
",",
"value",
",",
"dict",
")",
"if",
"prop",
"in",
"_complex_definitions",
":",
"comple... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | validate_complex_list | Default validation for Attribute Details data structure | gis_metadata/utils.py | def validate_complex_list(prop, value, xpath_map=None):
""" Default validation for Attribute Details data structure """
if value is not None:
validate_type(prop, value, (dict, list))
if prop in _complex_definitions:
complex_keys = _complex_definitions[prop]
else:
... | def validate_complex_list(prop, value, xpath_map=None):
""" Default validation for Attribute Details data structure """
if value is not None:
validate_type(prop, value, (dict, list))
if prop in _complex_definitions:
complex_keys = _complex_definitions[prop]
else:
... | [
"Default",
"validation",
"for",
"Attribute",
"Details",
"data",
"structure"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L592-L618 | [
"def",
"validate_complex_list",
"(",
"prop",
",",
"value",
",",
"xpath_map",
"=",
"None",
")",
":",
"if",
"value",
"is",
"not",
"None",
":",
"validate_type",
"(",
"prop",
",",
"value",
",",
"(",
"dict",
",",
"list",
")",
")",
"if",
"prop",
"in",
"_co... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | validate_dates | Default validation for Date Types data structure | gis_metadata/utils.py | def validate_dates(prop, value, xpath_map=None):
""" Default validation for Date Types data structure """
if value is not None:
validate_type(prop, value, dict)
date_keys = set(value)
if date_keys:
if DATE_TYPE not in date_keys or DATE_VALUES not in date_keys:
... | def validate_dates(prop, value, xpath_map=None):
""" Default validation for Date Types data structure """
if value is not None:
validate_type(prop, value, dict)
date_keys = set(value)
if date_keys:
if DATE_TYPE not in date_keys or DATE_VALUES not in date_keys:
... | [
"Default",
"validation",
"for",
"Date",
"Types",
"data",
"structure"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L621-L663 | [
"def",
"validate_dates",
"(",
"prop",
",",
"value",
",",
"xpath_map",
"=",
"None",
")",
":",
"if",
"value",
"is",
"not",
"None",
":",
"validate_type",
"(",
"prop",
",",
"value",
",",
"dict",
")",
"date_keys",
"=",
"set",
"(",
"value",
")",
"if",
"dat... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | validate_process_steps | Default validation for Process Steps data structure | gis_metadata/utils.py | def validate_process_steps(prop, value):
""" Default validation for Process Steps data structure """
if value is not None:
validate_type(prop, value, (dict, list))
procstep_keys = set(_complex_definitions[prop])
for idx, procstep in enumerate(wrap_value(value)):
ps_idx = p... | def validate_process_steps(prop, value):
""" Default validation for Process Steps data structure """
if value is not None:
validate_type(prop, value, (dict, list))
procstep_keys = set(_complex_definitions[prop])
for idx, procstep in enumerate(wrap_value(value)):
ps_idx = p... | [
"Default",
"validation",
"for",
"Process",
"Steps",
"data",
"structure"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L666-L691 | [
"def",
"validate_process_steps",
"(",
"prop",
",",
"value",
")",
":",
"if",
"value",
"is",
"not",
"None",
":",
"validate_type",
"(",
"prop",
",",
"value",
",",
"(",
"dict",
",",
"list",
")",
")",
"procstep_keys",
"=",
"set",
"(",
"_complex_definitions",
... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | validate_properties | Ensures the key set contains the base supported properties for a Parser
:param props: a set of property names to validate against those supported | gis_metadata/utils.py | def validate_properties(props, required):
"""
Ensures the key set contains the base supported properties for a Parser
:param props: a set of property names to validate against those supported
"""
props = set(props)
required = set(required or _supported_props)
if len(required.intersection(p... | def validate_properties(props, required):
"""
Ensures the key set contains the base supported properties for a Parser
:param props: a set of property names to validate against those supported
"""
props = set(props)
required = set(required or _supported_props)
if len(required.intersection(p... | [
"Ensures",
"the",
"key",
"set",
"contains",
"the",
"base",
"supported",
"properties",
"for",
"a",
"Parser",
":",
"param",
"props",
":",
"a",
"set",
"of",
"property",
"names",
"to",
"validate",
"against",
"those",
"supported"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L694-L707 | [
"def",
"validate_properties",
"(",
"props",
",",
"required",
")",
":",
"props",
"=",
"set",
"(",
"props",
")",
"required",
"=",
"set",
"(",
"required",
"or",
"_supported_props",
")",
"if",
"len",
"(",
"required",
".",
"intersection",
"(",
"props",
")",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | validate_type | Default validation for all types | gis_metadata/utils.py | def validate_type(prop, value, expected):
""" Default validation for all types """
# Validate on expected type(s), but ignore None: defaults handled elsewhere
if value is not None and not isinstance(value, expected):
_validation_error(prop, type(value).__name__, None, expected) | def validate_type(prop, value, expected):
""" Default validation for all types """
# Validate on expected type(s), but ignore None: defaults handled elsewhere
if value is not None and not isinstance(value, expected):
_validation_error(prop, type(value).__name__, None, expected) | [
"Default",
"validation",
"for",
"all",
"types"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L710-L715 | [
"def",
"validate_type",
"(",
"prop",
",",
"value",
",",
"expected",
")",
":",
"# Validate on expected type(s), but ignore None: defaults handled elsewhere",
"if",
"value",
"is",
"not",
"None",
"and",
"not",
"isinstance",
"(",
"value",
",",
"expected",
")",
":",
"_va... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | _validation_error | Default validation for updated properties | gis_metadata/utils.py | def _validation_error(prop, prop_type, prop_value, expected):
""" Default validation for updated properties """
if prop_type is None:
attrib = 'value'
assigned = prop_value
else:
attrib = 'type'
assigned = prop_type
raise ValidationError(
'Invalid property {attr... | def _validation_error(prop, prop_type, prop_value, expected):
""" Default validation for updated properties """
if prop_type is None:
attrib = 'value'
assigned = prop_value
else:
attrib = 'type'
assigned = prop_type
raise ValidationError(
'Invalid property {attr... | [
"Default",
"validation",
"for",
"updated",
"properties"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L718-L732 | [
"def",
"_validation_error",
"(",
"prop",
",",
"prop_type",
",",
"prop_value",
",",
"expected",
")",
":",
"if",
"prop_type",
"is",
"None",
":",
"attrib",
"=",
"'value'",
"assigned",
"=",
"prop_value",
"else",
":",
"attrib",
"=",
"'type'",
"assigned",
"=",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | ParserProperty.get_prop | Calls the getter with no arguments and returns its value | gis_metadata/utils.py | def get_prop(self, prop):
""" Calls the getter with no arguments and returns its value """
if self._parser is None:
raise ConfigurationError('Cannot call ParserProperty."get_prop" with no parser configured')
return self._parser(prop) if prop else self._parser() | def get_prop(self, prop):
""" Calls the getter with no arguments and returns its value """
if self._parser is None:
raise ConfigurationError('Cannot call ParserProperty."get_prop" with no parser configured')
return self._parser(prop) if prop else self._parser() | [
"Calls",
"the",
"getter",
"with",
"no",
"arguments",
"and",
"returns",
"its",
"value"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L765-L771 | [
"def",
"get_prop",
"(",
"self",
",",
"prop",
")",
":",
"if",
"self",
".",
"_parser",
"is",
"None",
":",
"raise",
"ConfigurationError",
"(",
"'Cannot call ParserProperty.\"get_prop\" with no parser configured'",
")",
"return",
"self",
".",
"_parser",
"(",
"prop",
"... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | ParserProperty.set_prop | Calls the setter with the specified keyword arguments for flexibility.
:param setter_args: must contain tree_to_update, prop, values
:return: None, or the value updated for complex values | gis_metadata/utils.py | def set_prop(self, **setter_args):
"""
Calls the setter with the specified keyword arguments for flexibility.
:param setter_args: must contain tree_to_update, prop, values
:return: None, or the value updated for complex values
"""
if self.xpath:
setter_args['... | def set_prop(self, **setter_args):
"""
Calls the setter with the specified keyword arguments for flexibility.
:param setter_args: must contain tree_to_update, prop, values
:return: None, or the value updated for complex values
"""
if self.xpath:
setter_args['... | [
"Calls",
"the",
"setter",
"with",
"the",
"specified",
"keyword",
"arguments",
"for",
"flexibility",
".",
":",
"param",
"setter_args",
":",
"must",
"contain",
"tree_to_update",
"prop",
"values",
":",
"return",
":",
"None",
"or",
"the",
"value",
"updated",
"for"... | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L773-L783 | [
"def",
"set_prop",
"(",
"self",
",",
"*",
"*",
"setter_args",
")",
":",
"if",
"self",
".",
"xpath",
":",
"setter_args",
"[",
"'xpaths'",
"]",
"=",
"self",
".",
"xpath",
"return",
"self",
".",
"_updater",
"(",
"*",
"*",
"setter_args",
")"
] | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | grouped_command | Given a list of commands (which are assumed groupable), return
a new command which is a batch (multi) command.
For ``set`` commands the outcome will be::
set_multi({key: value}, **kwargs)
For ``get`` and ``delete`` commands, the outcome will be::
get_multi(list_of_keys, **kwargs)
(O... | nydus/db/backends/memcache.py | def grouped_command(commands):
"""
Given a list of commands (which are assumed groupable), return
a new command which is a batch (multi) command.
For ``set`` commands the outcome will be::
set_multi({key: value}, **kwargs)
For ``get`` and ``delete`` commands, the outcome will be::
... | def grouped_command(commands):
"""
Given a list of commands (which are assumed groupable), return
a new command which is a batch (multi) command.
For ``set`` commands the outcome will be::
set_multi({key: value}, **kwargs)
For ``get`` and ``delete`` commands, the outcome will be::
... | [
"Given",
"a",
"list",
"of",
"commands",
"(",
"which",
"are",
"assumed",
"groupable",
")",
"return",
"a",
"new",
"command",
"which",
"is",
"a",
"batch",
"(",
"multi",
")",
"command",
"."
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/backends/memcache.py#L67-L94 | [
"def",
"grouped_command",
"(",
"commands",
")",
":",
"base",
"=",
"commands",
"[",
"0",
"]",
"name",
"=",
"base",
".",
"get_name",
"(",
")",
"multi_command",
"=",
"EventualCommand",
"(",
"'%s_multi'",
"%",
"name",
")",
"if",
"name",
"in",
"(",
"'get'",
... | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
train | can_group_commands | Returns a boolean representing whether these commands can be
grouped together or not.
A few things are taken into account for this decision:
For ``set`` commands:
- Are all arguments other than the key/value the same?
For ``delete`` and ``get`` commands:
- Are all arguments other than the k... | nydus/db/backends/memcache.py | def can_group_commands(command, next_command):
"""
Returns a boolean representing whether these commands can be
grouped together or not.
A few things are taken into account for this decision:
For ``set`` commands:
- Are all arguments other than the key/value the same?
For ``delete`` and ... | def can_group_commands(command, next_command):
"""
Returns a boolean representing whether these commands can be
grouped together or not.
A few things are taken into account for this decision:
For ``set`` commands:
- Are all arguments other than the key/value the same?
For ``delete`` and ... | [
"Returns",
"a",
"boolean",
"representing",
"whether",
"these",
"commands",
"can",
"be",
"grouped",
"together",
"or",
"not",
"."
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/backends/memcache.py#L97-L135 | [
"def",
"can_group_commands",
"(",
"command",
",",
"next_command",
")",
":",
"multi_capable_commands",
"=",
"(",
"'get'",
",",
"'set'",
",",
"'delete'",
")",
"if",
"next_command",
"is",
"None",
":",
"return",
"False",
"name",
"=",
"command",
".",
"get_name",
... | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
train | regroup_commands | Returns a list of tuples:
[(command_to_run, [list, of, commands])]
If the list of commands has a single item, the command was not grouped. | nydus/db/backends/memcache.py | def regroup_commands(commands):
"""
Returns a list of tuples:
[(command_to_run, [list, of, commands])]
If the list of commands has a single item, the command was not grouped.
"""
grouped = []
pending = []
def group_pending():
if not pending:
return
new... | def regroup_commands(commands):
"""
Returns a list of tuples:
[(command_to_run, [list, of, commands])]
If the list of commands has a single item, the command was not grouped.
"""
grouped = []
pending = []
def group_pending():
if not pending:
return
new... | [
"Returns",
"a",
"list",
"of",
"tuples",
":"
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/backends/memcache.py#L138-L182 | [
"def",
"regroup_commands",
"(",
"commands",
")",
":",
"grouped",
"=",
"[",
"]",
"pending",
"=",
"[",
"]",
"def",
"group_pending",
"(",
")",
":",
"if",
"not",
"pending",
":",
"return",
"new_command",
"=",
"grouped_command",
"(",
"pending",
")",
"result",
... | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.