repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
widdowquinn/pyani | pyani/pyani_jobs.py | JobGroup.generate_script | def generate_script(self):
"""Create the SGE script that will run the jobs in the JobGroup, with
the passed arguments.
"""
self.script = "" # Holds the script string
total = 1 # total number of jobs in this group
# for now, SGE_TASK_ID becomes TASK_I... | python | def generate_script(self):
"""Create the SGE script that will run the jobs in the JobGroup, with
the passed arguments.
"""
self.script = "" # Holds the script string
total = 1 # total number of jobs in this group
# for now, SGE_TASK_ID becomes TASK_I... | Create the SGE script that will run the jobs in the JobGroup, with
the passed arguments. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_jobs.py#L119-L154 |
widdowquinn/pyani | pyani/anim.py | generate_nucmer_jobs | def generate_nucmer_jobs(
filenames,
outdir=".",
nucmer_exe=pyani_config.NUCMER_DEFAULT,
filter_exe=pyani_config.FILTER_DEFAULT,
maxmatch=False,
jobprefix="ANINUCmer",
):
"""Return a list of Jobs describing NUCmer command-lines for ANIm
- filenames - a list of paths to input FASTA files... | python | def generate_nucmer_jobs(
filenames,
outdir=".",
nucmer_exe=pyani_config.NUCMER_DEFAULT,
filter_exe=pyani_config.FILTER_DEFAULT,
maxmatch=False,
jobprefix="ANINUCmer",
):
"""Return a list of Jobs describing NUCmer command-lines for ANIm
- filenames - a list of paths to input FASTA files... | Return a list of Jobs describing NUCmer command-lines for ANIm
- filenames - a list of paths to input FASTA files
- outdir - path to output directory
- nucmer_exe - location of the nucmer binary
- maxmatch - Boolean flag indicating to use NUCmer's -maxmatch option
Loop over all FASTA files, genera... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anim.py#L33-L61 |
widdowquinn/pyani | pyani/anim.py | generate_nucmer_commands | def generate_nucmer_commands(
filenames,
outdir=".",
nucmer_exe=pyani_config.NUCMER_DEFAULT,
filter_exe=pyani_config.FILTER_DEFAULT,
maxmatch=False,
):
"""Return a tuple of lists of NUCmer command-lines for ANIm
The first element is a list of NUCmer commands, the second a list
of delta_... | python | def generate_nucmer_commands(
filenames,
outdir=".",
nucmer_exe=pyani_config.NUCMER_DEFAULT,
filter_exe=pyani_config.FILTER_DEFAULT,
maxmatch=False,
):
"""Return a tuple of lists of NUCmer command-lines for ANIm
The first element is a list of NUCmer commands, the second a list
of delta_... | Return a tuple of lists of NUCmer command-lines for ANIm
The first element is a list of NUCmer commands, the second a list
of delta_filter_wrapper.py commands. These are ordered such that
commands are paired. The NUCmer commands should be run before
the delta-filter commands.
- filenames - a list ... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anim.py#L66-L96 |
widdowquinn/pyani | pyani/anim.py | construct_nucmer_cmdline | def construct_nucmer_cmdline(
fname1,
fname2,
outdir=".",
nucmer_exe=pyani_config.NUCMER_DEFAULT,
filter_exe=pyani_config.FILTER_DEFAULT,
maxmatch=False,
):
"""Returns a tuple of NUCmer and delta-filter commands
The split into a tuple was made necessary by changes to SGE/OGE. The
de... | python | def construct_nucmer_cmdline(
fname1,
fname2,
outdir=".",
nucmer_exe=pyani_config.NUCMER_DEFAULT,
filter_exe=pyani_config.FILTER_DEFAULT,
maxmatch=False,
):
"""Returns a tuple of NUCmer and delta-filter commands
The split into a tuple was made necessary by changes to SGE/OGE. The
de... | Returns a tuple of NUCmer and delta-filter commands
The split into a tuple was made necessary by changes to SGE/OGE. The
delta-filter command must now be run as a dependency of the NUCmer
command, and be wrapped in a Python script to capture STDOUT.
NOTE: This command-line writes output data to a subd... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anim.py#L101-L143 |
widdowquinn/pyani | pyani/anim.py | parse_delta | def parse_delta(filename):
"""Returns (alignment length, similarity errors) tuple from passed .delta.
- filename - path to the input .delta file
Extracts the aligned length and number of similarity errors for each
aligned uniquely-matched region, and returns the cumulative total for
each as a tupl... | python | def parse_delta(filename):
"""Returns (alignment length, similarity errors) tuple from passed .delta.
- filename - path to the input .delta file
Extracts the aligned length and number of similarity errors for each
aligned uniquely-matched region, and returns the cumulative total for
each as a tupl... | Returns (alignment length, similarity errors) tuple from passed .delta.
- filename - path to the input .delta file
Extracts the aligned length and number of similarity errors for each
aligned uniquely-matched region, and returns the cumulative total for
each as a tuple. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anim.py#L148-L165 |
widdowquinn/pyani | pyani/anim.py | process_deltadir | def process_deltadir(delta_dir, org_lengths, logger=None):
"""Returns a tuple of ANIm results for .deltas in passed directory.
- delta_dir - path to the directory containing .delta files
- org_lengths - dictionary of total sequence lengths, keyed by sequence
Returns the following pandas dataframes in ... | python | def process_deltadir(delta_dir, org_lengths, logger=None):
"""Returns a tuple of ANIm results for .deltas in passed directory.
- delta_dir - path to the directory containing .delta files
- org_lengths - dictionary of total sequence lengths, keyed by sequence
Returns the following pandas dataframes in ... | Returns a tuple of ANIm results for .deltas in passed directory.
- delta_dir - path to the directory containing .delta files
- org_lengths - dictionary of total sequence lengths, keyed by sequence
Returns the following pandas dataframes in an ANIResults object;
query sequences are rows, subject sequen... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anim.py#L169-L244 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | parse_cmdline | def parse_cmdline():
"""Parse command-line arguments"""
parser = ArgumentParser(prog="genbank_get_genomes_by_taxon.py")
parser.add_argument(
"-o",
"--outdir",
dest="outdirname",
required=True,
action="store",
default=None,
help="Output directory (requi... | python | def parse_cmdline():
"""Parse command-line arguments"""
parser = ArgumentParser(prog="genbank_get_genomes_by_taxon.py")
parser.add_argument(
"-o",
"--outdir",
dest="outdirname",
required=True,
action="store",
default=None,
help="Output directory (requi... | Parse command-line arguments | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L46-L125 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | set_ncbi_email | def set_ncbi_email():
"""Set contact email for NCBI."""
Entrez.email = args.email
logger.info("Set NCBI contact email to %s", args.email)
Entrez.tool = "genbank_get_genomes_by_taxon.py" | python | def set_ncbi_email():
"""Set contact email for NCBI."""
Entrez.email = args.email
logger.info("Set NCBI contact email to %s", args.email)
Entrez.tool = "genbank_get_genomes_by_taxon.py" | Set contact email for NCBI. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L139-L143 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | entrez_retry | def entrez_retry(func, *fnargs, **fnkwargs):
"""Retries the passed function up to the number of times specified
by args.retries
"""
tries, success = 0, False
while not success and tries < args.retries:
try:
output = func(*fnargs, **fnkwargs)
success = True
exc... | python | def entrez_retry(func, *fnargs, **fnkwargs):
"""Retries the passed function up to the number of times specified
by args.retries
"""
tries, success = 0, False
while not success and tries < args.retries:
try:
output = func(*fnargs, **fnkwargs)
success = True
exc... | Retries the passed function up to the number of times specified
by args.retries | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L187-L204 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | entrez_batch_webhistory | def entrez_batch_webhistory(record, expected, batchsize, *fnargs, **fnkwargs):
"""Recovers the Entrez data from a prior NCBI webhistory search, in
batches of defined size, using Efetch. Returns all results as a list.
- record: Entrez webhistory record
- expected: number of expected search returns
-... | python | def entrez_batch_webhistory(record, expected, batchsize, *fnargs, **fnkwargs):
"""Recovers the Entrez data from a prior NCBI webhistory search, in
batches of defined size, using Efetch. Returns all results as a list.
- record: Entrez webhistory record
- expected: number of expected search returns
-... | Recovers the Entrez data from a prior NCBI webhistory search, in
batches of defined size, using Efetch. Returns all results as a list.
- record: Entrez webhistory record
- expected: number of expected search returns
- batchsize: how many search returns to retrieve in a batch
- *fnargs: arguments to... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L208-L230 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | get_asm_uids | def get_asm_uids(taxon_uid):
"""Returns a set of NCBI UIDs associated with the passed taxon.
This query at NCBI returns all assemblies for the taxon subtree
rooted at the passed taxon_uid.
"""
query = "txid%s[Organism:exp]" % taxon_uid
logger.info("Entrez ESearch with query: %s", query)
# ... | python | def get_asm_uids(taxon_uid):
"""Returns a set of NCBI UIDs associated with the passed taxon.
This query at NCBI returns all assemblies for the taxon subtree
rooted at the passed taxon_uid.
"""
query = "txid%s[Organism:exp]" % taxon_uid
logger.info("Entrez ESearch with query: %s", query)
# ... | Returns a set of NCBI UIDs associated with the passed taxon.
This query at NCBI returns all assemblies for the taxon subtree
rooted at the passed taxon_uid. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L234-L259 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | extract_filestem | def extract_filestem(data):
"""Extract filestem from Entrez eSummary data.
Function expects esummary['DocumentSummarySet']['DocumentSummary'][0]
Some illegal characters may occur in AssemblyName - for these, a more
robust regex replace/escape may be required. Sadly, NCBI don't just
use standard pe... | python | def extract_filestem(data):
"""Extract filestem from Entrez eSummary data.
Function expects esummary['DocumentSummarySet']['DocumentSummary'][0]
Some illegal characters may occur in AssemblyName - for these, a more
robust regex replace/escape may be required. Sadly, NCBI don't just
use standard pe... | Extract filestem from Entrez eSummary data.
Function expects esummary['DocumentSummarySet']['DocumentSummary'][0]
Some illegal characters may occur in AssemblyName - for these, a more
robust regex replace/escape may be required. Sadly, NCBI don't just
use standard percent escapes, but instead replace ... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L263-L275 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | get_ncbi_asm | def get_ncbi_asm(asm_uid, fmt='fasta'):
"""Returns the NCBI AssemblyAccession and AssemblyName for the assembly
with passed UID, and organism data for class/label files also, as well
as accession, so we can track whether downloads fail because only the
most recent version is available..
AssemblyAcc... | python | def get_ncbi_asm(asm_uid, fmt='fasta'):
"""Returns the NCBI AssemblyAccession and AssemblyName for the assembly
with passed UID, and organism data for class/label files also, as well
as accession, so we can track whether downloads fail because only the
most recent version is available..
AssemblyAcc... | Returns the NCBI AssemblyAccession and AssemblyName for the assembly
with passed UID, and organism data for class/label files also, as well
as accession, so we can track whether downloads fail because only the
most recent version is available..
AssemblyAccession and AssemblyName are data fields in the ... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L279-L344 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | retrieve_asm_contigs | def retrieve_asm_contigs(filestem,
ftpstem="ftp://ftp.ncbi.nlm.nih.gov/genomes/all",
fmt='fasta'):
"""Downloads an assembly sequence to a local directory.
The filestem corresponds to <AA>_<AN>, where <AA> and <AN> are
AssemblyAccession and AssemblyName: dat... | python | def retrieve_asm_contigs(filestem,
ftpstem="ftp://ftp.ncbi.nlm.nih.gov/genomes/all",
fmt='fasta'):
"""Downloads an assembly sequence to a local directory.
The filestem corresponds to <AA>_<AN>, where <AA> and <AN> are
AssemblyAccession and AssemblyName: dat... | Downloads an assembly sequence to a local directory.
The filestem corresponds to <AA>_<AN>, where <AA> and <AN> are
AssemblyAccession and AssemblyName: data fields in the eSummary record.
These correspond to downloadable files for each assembly at
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GC[AF]/nnn/nnn/n... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L348-L477 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | write_contigs | def write_contigs(asm_uid, contig_uids, batchsize=10000):
"""Writes assembly contigs out to a single FASTA file in the script's
designated output directory.
FASTA records are returned, as GenBank and even GenBankWithParts format
records don't reliably give correct sequence in all cases.
The script... | python | def write_contigs(asm_uid, contig_uids, batchsize=10000):
"""Writes assembly contigs out to a single FASTA file in the script's
designated output directory.
FASTA records are returned, as GenBank and even GenBankWithParts format
records don't reliably give correct sequence in all cases.
The script... | Writes assembly contigs out to a single FASTA file in the script's
designated output directory.
FASTA records are returned, as GenBank and even GenBankWithParts format
records don't reliably give correct sequence in all cases.
The script returns two strings for each assembly, a 'class' and a 'label'
... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L481-L560 |
widdowquinn/pyani | bin/genbank_get_genomes_by_taxon.py | logreport_downloaded | def logreport_downloaded(accession, skippedlist, accessiondict, uidaccdict):
"""Reports to logger whether alternative assemblies for an accession that
was missing have been downloaded
"""
for vid in accessiondict[accession.split('.')[0]]:
if vid in skippedlist:
status = "NOT DOWNLOAD... | python | def logreport_downloaded(accession, skippedlist, accessiondict, uidaccdict):
"""Reports to logger whether alternative assemblies for an accession that
was missing have been downloaded
"""
for vid in accessiondict[accession.split('.')[0]]:
if vid in skippedlist:
status = "NOT DOWNLOAD... | Reports to logger whether alternative assemblies for an accession that
was missing have been downloaded | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/bin/genbank_get_genomes_by_taxon.py#L564-L573 |
widdowquinn/pyani | pyani/tetra.py | calculate_tetra_zscores | def calculate_tetra_zscores(infilenames):
"""Returns dictionary of TETRA Z-scores for each input file.
- infilenames - collection of paths to sequence files
"""
org_tetraz = {}
for filename in infilenames:
org = os.path.splitext(os.path.split(filename)[-1])[0]
org_tetraz[org] = calc... | python | def calculate_tetra_zscores(infilenames):
"""Returns dictionary of TETRA Z-scores for each input file.
- infilenames - collection of paths to sequence files
"""
org_tetraz = {}
for filename in infilenames:
org = os.path.splitext(os.path.split(filename)[-1])[0]
org_tetraz[org] = calc... | Returns dictionary of TETRA Z-scores for each input file.
- infilenames - collection of paths to sequence files | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/tetra.py#L33-L42 |
widdowquinn/pyani | pyani/tetra.py | calculate_tetra_zscore | def calculate_tetra_zscore(filename):
"""Returns TETRA Z-score for the sequence in the passed file.
- filename - path to sequence file
Calculates mono-, di-, tri- and tetranucleotide frequencies
for each sequence, on each strand, and follows Teeling et al. (2004)
in calculating a corresponding Z-s... | python | def calculate_tetra_zscore(filename):
"""Returns TETRA Z-score for the sequence in the passed file.
- filename - path to sequence file
Calculates mono-, di-, tri- and tetranucleotide frequencies
for each sequence, on each strand, and follows Teeling et al. (2004)
in calculating a corresponding Z-s... | Returns TETRA Z-score for the sequence in the passed file.
- filename - path to sequence file
Calculates mono-, di-, tri- and tetranucleotide frequencies
for each sequence, on each strand, and follows Teeling et al. (2004)
in calculating a corresponding Z-score for each observed
tetranucleotide fr... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/tetra.py#L46-L102 |
widdowquinn/pyani | pyani/tetra.py | calculate_correlations | def calculate_correlations(tetra_z):
"""Returns dataframe of Pearson correlation coefficients.
- tetra_z - dictionary of Z-scores, keyed by sequence ID
Calculates Pearson correlation coefficient from Z scores for each
tetranucleotide. This is done longhand here, which is fast enough,
but for robus... | python | def calculate_correlations(tetra_z):
"""Returns dataframe of Pearson correlation coefficients.
- tetra_z - dictionary of Z-scores, keyed by sequence ID
Calculates Pearson correlation coefficient from Z scores for each
tetranucleotide. This is done longhand here, which is fast enough,
but for robus... | Returns dataframe of Pearson correlation coefficients.
- tetra_z - dictionary of Z-scores, keyed by sequence ID
Calculates Pearson correlation coefficient from Z scores for each
tetranucleotide. This is done longhand here, which is fast enough,
but for robustness we might want to do something else... ... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/tetra.py#L118-L149 |
widdowquinn/pyani | pyani/pyani_tools.py | get_labels | def get_labels(filename, logger=None):
"""Returns a dictionary of alternative sequence labels, or None
- filename - path to file containing tab-separated table of labels
Input files should be formatted as <key>\t<label>, one pair per line.
"""
labeldict = {}
if filename is not None:
if... | python | def get_labels(filename, logger=None):
"""Returns a dictionary of alternative sequence labels, or None
- filename - path to file containing tab-separated table of labels
Input files should be formatted as <key>\t<label>, one pair per line.
"""
labeldict = {}
if filename is not None:
if... | Returns a dictionary of alternative sequence labels, or None
- filename - path to file containing tab-separated table of labels
Input files should be formatted as <key>\t<label>, one pair per line. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L131-L156 |
widdowquinn/pyani | pyani/pyani_tools.py | ANIResults.add_tot_length | def add_tot_length(self, qname, sname, value, sym=True):
"""Add a total length value to self.alignment_lengths."""
self.alignment_lengths.loc[qname, sname] = value
if sym:
self.alignment_lengths.loc[sname, qname] = value | python | def add_tot_length(self, qname, sname, value, sym=True):
"""Add a total length value to self.alignment_lengths."""
self.alignment_lengths.loc[qname, sname] = value
if sym:
self.alignment_lengths.loc[sname, qname] = value | Add a total length value to self.alignment_lengths. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L33-L37 |
widdowquinn/pyani | pyani/pyani_tools.py | ANIResults.add_sim_errors | def add_sim_errors(self, qname, sname, value, sym=True):
"""Add a similarity error value to self.similarity_errors."""
self.similarity_errors.loc[qname, sname] = value
if sym:
self.similarity_errors.loc[sname, qname] = value | python | def add_sim_errors(self, qname, sname, value, sym=True):
"""Add a similarity error value to self.similarity_errors."""
self.similarity_errors.loc[qname, sname] = value
if sym:
self.similarity_errors.loc[sname, qname] = value | Add a similarity error value to self.similarity_errors. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L39-L43 |
widdowquinn/pyani | pyani/pyani_tools.py | ANIResults.add_pid | def add_pid(self, qname, sname, value, sym=True):
"""Add a percentage identity value to self.percentage_identity."""
self.percentage_identity.loc[qname, sname] = value
if sym:
self.percentage_identity.loc[sname, qname] = value | python | def add_pid(self, qname, sname, value, sym=True):
"""Add a percentage identity value to self.percentage_identity."""
self.percentage_identity.loc[qname, sname] = value
if sym:
self.percentage_identity.loc[sname, qname] = value | Add a percentage identity value to self.percentage_identity. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L45-L49 |
widdowquinn/pyani | pyani/pyani_tools.py | ANIResults.add_coverage | def add_coverage(self, qname, sname, qcover, scover=None):
"""Add percentage coverage values to self.alignment_coverage."""
self.alignment_coverage.loc[qname, sname] = qcover
if scover:
self.alignment_coverage.loc[sname, qname] = scover | python | def add_coverage(self, qname, sname, qcover, scover=None):
"""Add percentage coverage values to self.alignment_coverage."""
self.alignment_coverage.loc[qname, sname] = qcover
if scover:
self.alignment_coverage.loc[sname, qname] = scover | Add percentage coverage values to self.alignment_coverage. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L51-L55 |
widdowquinn/pyani | pyani/pyani_tools.py | ANIResults.data | def data(self):
"""Return list of (dataframe, filestem) tuples."""
stemdict = {
"ANIm": pyani_config.ANIM_FILESTEMS,
"ANIb": pyani_config.ANIB_FILESTEMS,
"ANIblastall": pyani_config.ANIBLASTALL_FILESTEMS,
}
return zip(
(
sel... | python | def data(self):
"""Return list of (dataframe, filestem) tuples."""
stemdict = {
"ANIm": pyani_config.ANIM_FILESTEMS,
"ANIb": pyani_config.ANIB_FILESTEMS,
"ANIblastall": pyani_config.ANIBLASTALL_FILESTEMS,
}
return zip(
(
sel... | Return list of (dataframe, filestem) tuples. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L63-L79 |
widdowquinn/pyani | pyani/pyani_tools.py | BLASTcmds.build_db_cmd | def build_db_cmd(self, fname):
"""Return database format/build command"""
return self.funcs.db_func(fname, self.outdir, self.exes.format_exe)[0] | python | def build_db_cmd(self, fname):
"""Return database format/build command"""
return self.funcs.db_func(fname, self.outdir, self.exes.format_exe)[0] | Return database format/build command | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L117-L119 |
widdowquinn/pyani | pyani/pyani_tools.py | BLASTcmds.get_db_name | def get_db_name(self, fname):
"""Return database filename"""
return self.funcs.db_func(fname, self.outdir, self.exes.format_exe)[1] | python | def get_db_name(self, fname):
"""Return database filename"""
return self.funcs.db_func(fname, self.outdir, self.exes.format_exe)[1] | Return database filename | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L121-L123 |
widdowquinn/pyani | pyani/pyani_tools.py | BLASTcmds.build_blast_cmd | def build_blast_cmd(self, fname, dbname):
"""Return BLASTN command"""
return self.funcs.blastn_func(fname, dbname, self.outdir, self.exes.blast_exe) | python | def build_blast_cmd(self, fname, dbname):
"""Return BLASTN command"""
return self.funcs.blastn_func(fname, dbname, self.outdir, self.exes.blast_exe) | Return BLASTN command | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_tools.py#L125-L127 |
widdowquinn/pyani | pyani/anib.py | fragment_fasta_files | def fragment_fasta_files(infiles, outdirname, fragsize):
"""Chops sequences of the passed files into fragments, returns filenames.
- infiles - paths to each input sequence file
- outdirname - path to output directory
- fragsize - the size of sequence fragments
Takes every sequence from every file ... | python | def fragment_fasta_files(infiles, outdirname, fragsize):
"""Chops sequences of the passed files into fragments, returns filenames.
- infiles - paths to each input sequence file
- outdirname - path to output directory
- fragsize - the size of sequence fragments
Takes every sequence from every file ... | Chops sequences of the passed files into fragments, returns filenames.
- infiles - paths to each input sequence file
- outdirname - path to output directory
- fragsize - the size of sequence fragments
Takes every sequence from every file in infiles, and splits them into
consecutive fragments of le... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L100-L130 |
widdowquinn/pyani | pyani/anib.py | get_fraglength_dict | def get_fraglength_dict(fastafiles):
"""Returns dictionary of sequence fragment lengths, keyed by query name.
- fastafiles - list of FASTA input whole sequence files
Loops over input files and, for each, produces a dictionary with fragment
lengths, keyed by sequence ID. These are returned as a diction... | python | def get_fraglength_dict(fastafiles):
"""Returns dictionary of sequence fragment lengths, keyed by query name.
- fastafiles - list of FASTA input whole sequence files
Loops over input files and, for each, produces a dictionary with fragment
lengths, keyed by sequence ID. These are returned as a diction... | Returns dictionary of sequence fragment lengths, keyed by query name.
- fastafiles - list of FASTA input whole sequence files
Loops over input files and, for each, produces a dictionary with fragment
lengths, keyed by sequence ID. These are returned as a dictionary with
the keys being query IDs derive... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L134-L147 |
widdowquinn/pyani | pyani/anib.py | get_fragment_lengths | def get_fragment_lengths(fastafile):
"""Returns dictionary of sequence fragment lengths, keyed by fragment ID.
Biopython's SeqIO module is used to parse all sequences in the FASTA
file.
NOTE: ambiguity symbols are not discounted.
"""
fraglengths = {}
for seq in SeqIO.parse(fastafile, "fast... | python | def get_fragment_lengths(fastafile):
"""Returns dictionary of sequence fragment lengths, keyed by fragment ID.
Biopython's SeqIO module is used to parse all sequences in the FASTA
file.
NOTE: ambiguity symbols are not discounted.
"""
fraglengths = {}
for seq in SeqIO.parse(fastafile, "fast... | Returns dictionary of sequence fragment lengths, keyed by fragment ID.
Biopython's SeqIO module is used to parse all sequences in the FASTA
file.
NOTE: ambiguity symbols are not discounted. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L151-L162 |
widdowquinn/pyani | pyani/anib.py | build_db_jobs | def build_db_jobs(infiles, blastcmds):
"""Returns dictionary of db-building commands, keyed by dbname."""
dbjobdict = {} # Dict of database construction jobs, keyed by filename
# Create dictionary of database building jobs, keyed by db name
# defining jobnum for later use as last job index used
for... | python | def build_db_jobs(infiles, blastcmds):
"""Returns dictionary of db-building commands, keyed by dbname."""
dbjobdict = {} # Dict of database construction jobs, keyed by filename
# Create dictionary of database building jobs, keyed by db name
# defining jobnum for later use as last job index used
for... | Returns dictionary of db-building commands, keyed by dbname. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L166-L175 |
widdowquinn/pyani | pyani/anib.py | make_blastcmd_builder | def make_blastcmd_builder(
mode, outdir, format_exe=None, blast_exe=None, prefix="ANIBLAST"
):
"""Returns BLASTcmds object for construction of BLAST commands."""
if mode == "ANIb": # BLAST/formatting executable depends on mode
blastcmds = BLASTcmds(
BLASTfunctions(construct_makeblastdb_... | python | def make_blastcmd_builder(
mode, outdir, format_exe=None, blast_exe=None, prefix="ANIBLAST"
):
"""Returns BLASTcmds object for construction of BLAST commands."""
if mode == "ANIb": # BLAST/formatting executable depends on mode
blastcmds = BLASTcmds(
BLASTfunctions(construct_makeblastdb_... | Returns BLASTcmds object for construction of BLAST commands. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L178-L202 |
widdowquinn/pyani | pyani/anib.py | make_job_graph | def make_job_graph(infiles, fragfiles, blastcmds):
"""Return a job dependency graph, based on the passed input sequence files.
- infiles - a list of paths to input FASTA files
- fragfiles - a list of paths to fragmented input FASTA files
By default, will run ANIb - it *is* possible to make a mess of p... | python | def make_job_graph(infiles, fragfiles, blastcmds):
"""Return a job dependency graph, based on the passed input sequence files.
- infiles - a list of paths to input FASTA files
- fragfiles - a list of paths to fragmented input FASTA files
By default, will run ANIb - it *is* possible to make a mess of p... | Return a job dependency graph, based on the passed input sequence files.
- infiles - a list of paths to input FASTA files
- fragfiles - a list of paths to fragmented input FASTA files
By default, will run ANIb - it *is* possible to make a mess of passing the
wrong executable for the mode you're using.... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L206-L246 |
widdowquinn/pyani | pyani/anib.py | generate_blastdb_commands | def generate_blastdb_commands(filenames, outdir, blastdb_exe=None, mode="ANIb"):
"""Return a list of makeblastdb command-lines for ANIb/ANIblastall
- filenames - a list of paths to input FASTA files
- outdir - path to output directory
- blastdb_exe - path to the makeblastdb executable
"""
if mo... | python | def generate_blastdb_commands(filenames, outdir, blastdb_exe=None, mode="ANIb"):
"""Return a list of makeblastdb command-lines for ANIb/ANIblastall
- filenames - a list of paths to input FASTA files
- outdir - path to output directory
- blastdb_exe - path to the makeblastdb executable
"""
if mo... | Return a list of makeblastdb command-lines for ANIb/ANIblastall
- filenames - a list of paths to input FASTA files
- outdir - path to output directory
- blastdb_exe - path to the makeblastdb executable | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L250-L267 |
widdowquinn/pyani | pyani/anib.py | construct_makeblastdb_cmd | def construct_makeblastdb_cmd(
filename, outdir, blastdb_exe=pyani_config.MAKEBLASTDB_DEFAULT
):
"""Returns a single makeblastdb command.
- filename - input filename
- blastdb_exe - path to the makeblastdb executable
"""
title = os.path.splitext(os.path.split(filename)[-1])[0]
outfilename =... | python | def construct_makeblastdb_cmd(
filename, outdir, blastdb_exe=pyani_config.MAKEBLASTDB_DEFAULT
):
"""Returns a single makeblastdb command.
- filename - input filename
- blastdb_exe - path to the makeblastdb executable
"""
title = os.path.splitext(os.path.split(filename)[-1])[0]
outfilename =... | Returns a single makeblastdb command.
- filename - input filename
- blastdb_exe - path to the makeblastdb executable | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L271-L286 |
widdowquinn/pyani | pyani/anib.py | construct_formatdb_cmd | def construct_formatdb_cmd(filename, outdir, blastdb_exe=pyani_config.FORMATDB_DEFAULT):
"""Returns a single formatdb command.
- filename - input filename
- blastdb_exe - path to the formatdb executable
"""
title = os.path.splitext(os.path.split(filename)[-1])[0]
newfilename = os.path.join(outd... | python | def construct_formatdb_cmd(filename, outdir, blastdb_exe=pyani_config.FORMATDB_DEFAULT):
"""Returns a single formatdb command.
- filename - input filename
- blastdb_exe - path to the formatdb executable
"""
title = os.path.splitext(os.path.split(filename)[-1])[0]
newfilename = os.path.join(outd... | Returns a single formatdb command.
- filename - input filename
- blastdb_exe - path to the formatdb executable | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L290-L302 |
widdowquinn/pyani | pyani/anib.py | generate_blastn_commands | def generate_blastn_commands(filenames, outdir, blast_exe=None, mode="ANIb"):
"""Return a list of blastn command-lines for ANIm
- filenames - a list of paths to fragmented input FASTA files
- outdir - path to output directory
- blastn_exe - path to BLASTN executable
Assumes that the fragment seque... | python | def generate_blastn_commands(filenames, outdir, blast_exe=None, mode="ANIb"):
"""Return a list of blastn command-lines for ANIm
- filenames - a list of paths to fragmented input FASTA files
- outdir - path to output directory
- blastn_exe - path to BLASTN executable
Assumes that the fragment seque... | Return a list of blastn command-lines for ANIm
- filenames - a list of paths to fragmented input FASTA files
- outdir - path to output directory
- blastn_exe - path to BLASTN executable
Assumes that the fragment sequence input filenames have the form
ACCESSION-fragments.ext, where the correspondin... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L306-L337 |
widdowquinn/pyani | pyani/anib.py | construct_blastn_cmdline | def construct_blastn_cmdline(
fname1, fname2, outdir, blastn_exe=pyani_config.BLASTN_DEFAULT
):
"""Returns a single blastn command.
- filename - input filename
- blastn_exe - path to BLASTN executable
"""
fstem1 = os.path.splitext(os.path.split(fname1)[-1])[0]
fstem2 = os.path.splitext(os.p... | python | def construct_blastn_cmdline(
fname1, fname2, outdir, blastn_exe=pyani_config.BLASTN_DEFAULT
):
"""Returns a single blastn command.
- filename - input filename
- blastn_exe - path to BLASTN executable
"""
fstem1 = os.path.splitext(os.path.split(fname1)[-1])[0]
fstem2 = os.path.splitext(os.p... | Returns a single blastn command.
- filename - input filename
- blastn_exe - path to BLASTN executable | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L341-L360 |
widdowquinn/pyani | pyani/anib.py | construct_blastall_cmdline | def construct_blastall_cmdline(
fname1, fname2, outdir, blastall_exe=pyani_config.BLASTALL_DEFAULT
):
"""Returns a single blastall command.
- blastall_exe - path to BLASTALL executable
"""
fstem1 = os.path.splitext(os.path.split(fname1)[-1])[0]
fstem2 = os.path.splitext(os.path.split(fname2)[-1... | python | def construct_blastall_cmdline(
fname1, fname2, outdir, blastall_exe=pyani_config.BLASTALL_DEFAULT
):
"""Returns a single blastall command.
- blastall_exe - path to BLASTALL executable
"""
fstem1 = os.path.splitext(os.path.split(fname1)[-1])[0]
fstem2 = os.path.splitext(os.path.split(fname2)[-1... | Returns a single blastall command.
- blastall_exe - path to BLASTALL executable | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L364-L380 |
widdowquinn/pyani | pyani/anib.py | process_blast | def process_blast(
blast_dir,
org_lengths,
fraglengths=None,
mode="ANIb",
identity=0.3,
coverage=0.7,
logger=None,
):
"""Returns a tuple of ANIb results for .blast_tab files in the output dir.
- blast_dir - path to the directory containing .blast_tab files
- org_lengths - the ba... | python | def process_blast(
blast_dir,
org_lengths,
fraglengths=None,
mode="ANIb",
identity=0.3,
coverage=0.7,
logger=None,
):
"""Returns a tuple of ANIb results for .blast_tab files in the output dir.
- blast_dir - path to the directory containing .blast_tab files
- org_lengths - the ba... | Returns a tuple of ANIb results for .blast_tab files in the output dir.
- blast_dir - path to the directory containing .blast_tab files
- org_lengths - the base count for each input sequence
- fraglengths - dictionary of query sequence fragment lengths, only
needed for BLASTALL output
- mode - pars... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L384-L453 |
widdowquinn/pyani | pyani/anib.py | parse_blast_tab | def parse_blast_tab(filename, fraglengths, identity, coverage, mode="ANIb"):
"""Returns (alignment length, similarity errors, mean_pid) tuple
from .blast_tab
- filename - path to .blast_tab file
Calculate the alignment length and total number of similarity errors (as
we would with ANIm), as well a... | python | def parse_blast_tab(filename, fraglengths, identity, coverage, mode="ANIb"):
"""Returns (alignment length, similarity errors, mean_pid) tuple
from .blast_tab
- filename - path to .blast_tab file
Calculate the alignment length and total number of similarity errors (as
we would with ANIm), as well a... | Returns (alignment length, similarity errors, mean_pid) tuple
from .blast_tab
- filename - path to .blast_tab file
Calculate the alignment length and total number of similarity errors (as
we would with ANIm), as well as the Goris et al.-defined mean identity
of all valid BLAST matches for the pass... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/anib.py#L457-L551 |
widdowquinn/pyani | pyani/run_sge.py | split_seq | def split_seq(iterable, size):
"""Splits a passed iterable into chunks of a given size."""
elm = iter(iterable)
item = list(itertools.islice(elm, size))
while item:
yield item
item = list(itertools.islice(elm, size)) | python | def split_seq(iterable, size):
"""Splits a passed iterable into chunks of a given size."""
elm = iter(iterable)
item = list(itertools.islice(elm, size))
while item:
yield item
item = list(itertools.islice(elm, size)) | Splits a passed iterable into chunks of a given size. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L23-L29 |
widdowquinn/pyani | pyani/run_sge.py | build_joblist | def build_joblist(jobgraph):
"""Returns a list of jobs, from a passed jobgraph."""
jobset = set()
for job in jobgraph:
jobset = populate_jobset(job, jobset, depth=1)
return list(jobset) | python | def build_joblist(jobgraph):
"""Returns a list of jobs, from a passed jobgraph."""
jobset = set()
for job in jobgraph:
jobset = populate_jobset(job, jobset, depth=1)
return list(jobset) | Returns a list of jobs, from a passed jobgraph. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L33-L38 |
widdowquinn/pyani | pyani/run_sge.py | compile_jobgroups_from_joblist | def compile_jobgroups_from_joblist(joblist, jgprefix, sgegroupsize):
"""Return list of jobgroups, rather than list of jobs."""
jobcmds = defaultdict(list)
for job in joblist:
jobcmds[job.command.split(' ', 1)[0]].append(job.command)
jobgroups = []
for cmds in list(jobcmds.items()):
#... | python | def compile_jobgroups_from_joblist(joblist, jgprefix, sgegroupsize):
"""Return list of jobgroups, rather than list of jobs."""
jobcmds = defaultdict(list)
for job in joblist:
jobcmds[job.command.split(' ', 1)[0]].append(job.command)
jobgroups = []
for cmds in list(jobcmds.items()):
#... | Return list of jobgroups, rather than list of jobs. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L42-L58 |
widdowquinn/pyani | pyani/run_sge.py | run_dependency_graph | def run_dependency_graph(jobgraph, logger=None, jgprefix="ANIm_SGE_JG",
sgegroupsize=10000, sgeargs=None):
"""Creates and runs GridEngine scripts for jobs based on the passed
jobgraph.
- jobgraph - list of jobs, which may have dependencies.
- verbose - flag for multiprocessing ... | python | def run_dependency_graph(jobgraph, logger=None, jgprefix="ANIm_SGE_JG",
sgegroupsize=10000, sgeargs=None):
"""Creates and runs GridEngine scripts for jobs based on the passed
jobgraph.
- jobgraph - list of jobs, which may have dependencies.
- verbose - flag for multiprocessing ... | Creates and runs GridEngine scripts for jobs based on the passed
jobgraph.
- jobgraph - list of jobs, which may have dependencies.
- verbose - flag for multiprocessing verbosity
- logger - a logger module logger (optional)
- jgprefix - a prefix for the submitted jobs, in the scheduler
- sgegrou... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L62-L112 |
widdowquinn/pyani | pyani/run_sge.py | populate_jobset | def populate_jobset(job, jobset, depth):
""" Creates a set of jobs, containing jobs at difference depths of the
dependency tree, retaining dependencies as strings, not Jobs.
"""
jobset.add(job)
if len(job.dependencies) == 0:
return jobset
for j in job.dependencies:
jobset = popul... | python | def populate_jobset(job, jobset, depth):
""" Creates a set of jobs, containing jobs at difference depths of the
dependency tree, retaining dependencies as strings, not Jobs.
"""
jobset.add(job)
if len(job.dependencies) == 0:
return jobset
for j in job.dependencies:
jobset = popul... | Creates a set of jobs, containing jobs at difference depths of the
dependency tree, retaining dependencies as strings, not Jobs. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L115-L124 |
widdowquinn/pyani | pyani/run_sge.py | build_directories | def build_directories(root_dir):
"""Constructs the subdirectories output, stderr, stdout, and jobs in the
passed root directory. These subdirectories have the following roles:
jobs Stores the scripts for each job
stderr Stores the stderr output from SGE
stdout ... | python | def build_directories(root_dir):
"""Constructs the subdirectories output, stderr, stdout, and jobs in the
passed root directory. These subdirectories have the following roles:
jobs Stores the scripts for each job
stderr Stores the stderr output from SGE
stdout ... | Constructs the subdirectories output, stderr, stdout, and jobs in the
passed root directory. These subdirectories have the following roles:
jobs Stores the scripts for each job
stderr Stores the stderr output from SGE
stdout Stores the stdout output from SGE
... | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L127-L146 |
widdowquinn/pyani | pyani/run_sge.py | build_job_scripts | def build_job_scripts(root_dir, jobs):
"""Constructs the script for each passed Job in the jobs iterable
- root_dir Path to output directory
"""
# Loop over the job list, creating each job script in turn, and then adding
# scriptPath to the Job object
for job in jobs:
scriptpath = ... | python | def build_job_scripts(root_dir, jobs):
"""Constructs the script for each passed Job in the jobs iterable
- root_dir Path to output directory
"""
# Loop over the job list, creating each job script in turn, and then adding
# scriptPath to the Job object
for job in jobs:
scriptpath = ... | Constructs the script for each passed Job in the jobs iterable
- root_dir Path to output directory | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L149-L160 |
widdowquinn/pyani | pyani/run_sge.py | extract_submittable_jobs | def extract_submittable_jobs(waiting):
"""Obtain a list of jobs that are able to be submitted from the passed
list of pending jobs
- waiting List of Job objects
"""
submittable = set() # Holds jobs that are able to be submitted
# Loop over each job, and check all the subjob... | python | def extract_submittable_jobs(waiting):
"""Obtain a list of jobs that are able to be submitted from the passed
list of pending jobs
- waiting List of Job objects
"""
submittable = set() # Holds jobs that are able to be submitted
# Loop over each job, and check all the subjob... | Obtain a list of jobs that are able to be submitted from the passed
list of pending jobs
- waiting List of Job objects | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L163-L178 |
widdowquinn/pyani | pyani/run_sge.py | submit_safe_jobs | def submit_safe_jobs(root_dir, jobs, sgeargs=None):
"""Submit the passed list of jobs to the Grid Engine server, using the
passed directory as the root for scheduler output.
- root_dir Path to output directory
- jobs Iterable of Job objects
"""
# Loop over each job, constructing S... | python | def submit_safe_jobs(root_dir, jobs, sgeargs=None):
"""Submit the passed list of jobs to the Grid Engine server, using the
passed directory as the root for scheduler output.
- root_dir Path to output directory
- jobs Iterable of Job objects
"""
# Loop over each job, constructing S... | Submit the passed list of jobs to the Grid Engine server, using the
passed directory as the root for scheduler output.
- root_dir Path to output directory
- jobs Iterable of Job objects | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L181-L222 |
widdowquinn/pyani | pyani/run_sge.py | submit_jobs | def submit_jobs(root_dir, jobs, sgeargs=None):
""" Submit each of the passed jobs to the SGE server, using the passed
directory as root for SGE output.
- root_dir Path to output directory
- jobs List of Job objects
"""
waiting = list(jobs) # List of jobs still to... | python | def submit_jobs(root_dir, jobs, sgeargs=None):
""" Submit each of the passed jobs to the SGE server, using the passed
directory as root for SGE output.
- root_dir Path to output directory
- jobs List of Job objects
"""
waiting = list(jobs) # List of jobs still to... | Submit each of the passed jobs to the SGE server, using the passed
directory as root for SGE output.
- root_dir Path to output directory
- jobs List of Job objects | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L225-L241 |
widdowquinn/pyani | pyani/run_sge.py | build_and_submit_jobs | def build_and_submit_jobs(root_dir, jobs, sgeargs=None):
"""Submits the passed iterable of Job objects to SGE, placing SGE's
output in the passed root directory
- root_dir Root directory for SGE and job output
- jobs List of Job objects, describing each job to be submitted
- sgeargs Addi... | python | def build_and_submit_jobs(root_dir, jobs, sgeargs=None):
"""Submits the passed iterable of Job objects to SGE, placing SGE's
output in the passed root directory
- root_dir Root directory for SGE and job output
- jobs List of Job objects, describing each job to be submitted
- sgeargs Addi... | Submits the passed iterable of Job objects to SGE, placing SGE's
output in the passed root directory
- root_dir Root directory for SGE and job output
- jobs List of Job objects, describing each job to be submitted
- sgeargs Additional arguments to qsub | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/run_sge.py#L244-L260 |
widdowquinn/pyani | pyani/pyani_config.py | params_mpl | def params_mpl(df):
"""Returns dict of matplotlib parameters, dependent on dataframe."""
return {'ANIb_alignment_lengths': ('afmhot', df.values.min(),
df.values.max()),
'ANIb_percentage_identity': ('spbnd_BuRd', 0, 1),
'ANIb_alignment_coverage': ('B... | python | def params_mpl(df):
"""Returns dict of matplotlib parameters, dependent on dataframe."""
return {'ANIb_alignment_lengths': ('afmhot', df.values.min(),
df.values.max()),
'ANIb_percentage_identity': ('spbnd_BuRd', 0, 1),
'ANIb_alignment_coverage': ('B... | Returns dict of matplotlib parameters, dependent on dataframe. | https://github.com/widdowquinn/pyani/blob/2b24ec971401e04024bba896e4011984fe3f53f0/pyani/pyani_config.py#L107-L130 |
datapythonista/mnist | mnist/__init__.py | download_file | def download_file(fname, target_dir=None, force=False):
"""Download fname from the datasets_url, and save it to target_dir,
unless the file already exists, and force is False.
Parameters
----------
fname : str
Name of the file to download
target_dir : str
Directory where to sto... | python | def download_file(fname, target_dir=None, force=False):
"""Download fname from the datasets_url, and save it to target_dir,
unless the file already exists, and force is False.
Parameters
----------
fname : str
Name of the file to download
target_dir : str
Directory where to sto... | Download fname from the datasets_url, and save it to target_dir,
unless the file already exists, and force is False.
Parameters
----------
fname : str
Name of the file to download
target_dir : str
Directory where to store the file
force : bool
Force downloading the fil... | https://github.com/datapythonista/mnist/blob/d91df2b27ee62d07396b5b64c7cfead59833b563/mnist/__init__.py#L34-L61 |
datapythonista/mnist | mnist/__init__.py | parse_idx | def parse_idx(fd):
"""Parse an IDX file, and return it as a numpy array.
Parameters
----------
fd : file
File descriptor of the IDX file to parse
endian : str
Byte order of the IDX file. See [1] for available options
Returns
-------
data : numpy.ndarray
Numpy a... | python | def parse_idx(fd):
"""Parse an IDX file, and return it as a numpy array.
Parameters
----------
fd : file
File descriptor of the IDX file to parse
endian : str
Byte order of the IDX file. See [1] for available options
Returns
-------
data : numpy.ndarray
Numpy a... | Parse an IDX file, and return it as a numpy array.
Parameters
----------
fd : file
File descriptor of the IDX file to parse
endian : str
Byte order of the IDX file. See [1] for available options
Returns
-------
data : numpy.ndarray
Numpy array with the dimensions a... | https://github.com/datapythonista/mnist/blob/d91df2b27ee62d07396b5b64c7cfead59833b563/mnist/__init__.py#L64-L120 |
datapythonista/mnist | mnist/__init__.py | download_and_parse_mnist_file | def download_and_parse_mnist_file(fname, target_dir=None, force=False):
"""Download the IDX file named fname from the URL specified in dataset_url
and return it as a numpy array.
Parameters
----------
fname : str
File name to download and parse
target_dir : str
Directory where ... | python | def download_and_parse_mnist_file(fname, target_dir=None, force=False):
"""Download the IDX file named fname from the URL specified in dataset_url
and return it as a numpy array.
Parameters
----------
fname : str
File name to download and parse
target_dir : str
Directory where ... | Download the IDX file named fname from the URL specified in dataset_url
and return it as a numpy array.
Parameters
----------
fname : str
File name to download and parse
target_dir : str
Directory where to store the file
force : bool
Force downloading the file, if it a... | https://github.com/datapythonista/mnist/blob/d91df2b27ee62d07396b5b64c7cfead59833b563/mnist/__init__.py#L123-L146 |
Bogdanp/anom-py | anom/adapters/memcache_adapter.py | MemcacheAdapter._transactions | def _transactions(self):
"list[Transaction]: The current stack of Transactions."
transactions = getattr(self._state, "transactions", None)
if transactions is None:
transactions = self._state.transactions = []
return transactions | python | def _transactions(self):
"list[Transaction]: The current stack of Transactions."
transactions = getattr(self._state, "transactions", None)
if transactions is None:
transactions = self._state.transactions = []
return transactions | list[Transaction]: The current stack of Transactions. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/adapters/memcache_adapter.py#L76-L81 |
Bogdanp/anom-py | anom/transaction.py | transactional | def transactional(*, adapter=None, retries=3, propagation=Transaction.Propagation.Nested):
"""Decorates functions so that all of their operations (except for
queries) run inside a Datastore transaction.
Parameters:
adapter(Adapter, optional): The Adapter to use when running the
transaction. ... | python | def transactional(*, adapter=None, retries=3, propagation=Transaction.Propagation.Nested):
"""Decorates functions so that all of their operations (except for
queries) run inside a Datastore transaction.
Parameters:
adapter(Adapter, optional): The Adapter to use when running the
transaction. ... | Decorates functions so that all of their operations (except for
queries) run inside a Datastore transaction.
Parameters:
adapter(Adapter, optional): The Adapter to use when running the
transaction. Defaults to the current adapter.
retries(int, optional): The number of times to retry the
... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/transaction.py#L82-L131 |
Bogdanp/anom-py | anom/query.py | QueryOptions.batch_size | def batch_size(self):
"""int: The number of results to fetch per batch. Clamped to
limit if limit is set and is smaller than the given batch
size.
"""
batch_size = self.get("batch_size", DEFAULT_BATCH_SIZE)
if self.limit is not None:
return min(self.limit, ba... | python | def batch_size(self):
"""int: The number of results to fetch per batch. Clamped to
limit if limit is set and is smaller than the given batch
size.
"""
batch_size = self.get("batch_size", DEFAULT_BATCH_SIZE)
if self.limit is not None:
return min(self.limit, ba... | int: The number of results to fetch per batch. Clamped to
limit if limit is set and is smaller than the given batch
size. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/query.py#L46-L54 |
Bogdanp/anom-py | anom/query.py | Pages.fetch_next_page | def fetch_next_page(self):
"""Fetch the next Page of results.
Returns:
Page: The next page of results.
"""
for page in self:
return page
else:
return Page(self._resultset.cursor, iter(())) | python | def fetch_next_page(self):
"""Fetch the next Page of results.
Returns:
Page: The next page of results.
"""
for page in self:
return page
else:
return Page(self._resultset.cursor, iter(())) | Fetch the next Page of results.
Returns:
Page: The next page of results. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/query.py#L204-L213 |
Bogdanp/anom-py | anom/query.py | Query.count | def count(self, *, page_size=DEFAULT_BATCH_SIZE, **options):
"""Counts the number of entities that match this query.
Note:
Since Datastore doesn't provide a native way to count
entities by query, this method paginates through all the
entities' keys and counts them.
... | python | def count(self, *, page_size=DEFAULT_BATCH_SIZE, **options):
"""Counts the number of entities that match this query.
Note:
Since Datastore doesn't provide a native way to count
entities by query, this method paginates through all the
entities' keys and counts them.
... | Counts the number of entities that match this query.
Note:
Since Datastore doesn't provide a native way to count
entities by query, this method paginates through all the
entities' keys and counts them.
Parameters:
\**options(QueryOptions, optional)
Retu... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/query.py#L383-L401 |
Bogdanp/anom-py | anom/query.py | Query.delete | def delete(self, *, page_size=DEFAULT_BATCH_SIZE, **options):
"""Deletes all the entities that match this query.
Note:
Since Datasotre doesn't provide a native way to delete
entities by query, this method paginates through all the
entities' keys and issues a single delete_... | python | def delete(self, *, page_size=DEFAULT_BATCH_SIZE, **options):
"""Deletes all the entities that match this query.
Note:
Since Datasotre doesn't provide a native way to delete
entities by query, this method paginates through all the
entities' keys and issues a single delete_... | Deletes all the entities that match this query.
Note:
Since Datasotre doesn't provide a native way to delete
entities by query, this method paginates through all the
entities' keys and issues a single delete_multi call per
page.
Parameters:
\**options(... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/query.py#L403-L427 |
Bogdanp/anom-py | anom/query.py | Query.get | def get(self, **options):
"""Run this query and get the first result.
Parameters:
\**options(QueryOptions, optional)
Returns:
Model: An entity or None if there were no results.
"""
sub_query = self.with_limit(1)
options = QueryOptions(sub_query).repl... | python | def get(self, **options):
"""Run this query and get the first result.
Parameters:
\**options(QueryOptions, optional)
Returns:
Model: An entity or None if there were no results.
"""
sub_query = self.with_limit(1)
options = QueryOptions(sub_query).repl... | Run this query and get the first result.
Parameters:
\**options(QueryOptions, optional)
Returns:
Model: An entity or None if there were no results. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/query.py#L429-L442 |
Bogdanp/anom-py | anom/query.py | Query.paginate | def paginate(self, *, page_size, **options):
"""Run this query and return a page iterator.
Parameters:
page_size(int): The number of entities to fetch per page.
\**options(QueryOptions, optional)
Returns:
Pages: An iterator for this query's pages of results.
... | python | def paginate(self, *, page_size, **options):
"""Run this query and return a page iterator.
Parameters:
page_size(int): The number of entities to fetch per page.
\**options(QueryOptions, optional)
Returns:
Pages: An iterator for this query's pages of results.
... | Run this query and return a page iterator.
Parameters:
page_size(int): The number of entities to fetch per page.
\**options(QueryOptions, optional)
Returns:
Pages: An iterator for this query's pages of results. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/query.py#L455-L465 |
Bogdanp/anom-py | anom/conditions.py | is_none | def is_none(entity, prop, name):
"bool: True if the value of a property is None."
return is_not_empty(entity, prop, name) and getattr(entity, name) is None | python | def is_none(entity, prop, name):
"bool: True if the value of a property is None."
return is_not_empty(entity, prop, name) and getattr(entity, name) is None | bool: True if the value of a property is None. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/conditions.py#L21-L23 |
Bogdanp/anom-py | anom/conditions.py | is_not_none | def is_not_none(entity, prop, name):
"bool: True if the value of a property is not None."
return is_not_empty(entity, prop, name) and name in entity._data and getattr(entity, name) is not None | python | def is_not_none(entity, prop, name):
"bool: True if the value of a property is not None."
return is_not_empty(entity, prop, name) and name in entity._data and getattr(entity, name) is not None | bool: True if the value of a property is not None. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/conditions.py#L26-L28 |
Bogdanp/anom-py | anom/conditions.py | is_true | def is_true(entity, prop, name):
"bool: True if the value of a property is True."
return is_not_empty(entity, prop, name) and name in entity._data and bool(getattr(entity, name)) | python | def is_true(entity, prop, name):
"bool: True if the value of a property is True."
return is_not_empty(entity, prop, name) and name in entity._data and bool(getattr(entity, name)) | bool: True if the value of a property is True. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/conditions.py#L31-L33 |
Bogdanp/anom-py | anom/conditions.py | is_false | def is_false(entity, prop, name):
"bool: True if the value of a property is False."
return is_not_empty(entity, prop, name) and name in entity._data and not bool(getattr(entity, name)) | python | def is_false(entity, prop, name):
"bool: True if the value of a property is False."
return is_not_empty(entity, prop, name) and name in entity._data and not bool(getattr(entity, name)) | bool: True if the value of a property is False. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/conditions.py#L36-L38 |
Bogdanp/anom-py | anom/namespaces.py | namespace | def namespace(namespace):
"""Context manager for stacking the current thread-local default
namespace. Exiting the context sets the thread-local default
namespace back to the previously-set namespace. If there is no
previous namespace, then the thread-local namespace is cleared.
Example:
>>>... | python | def namespace(namespace):
"""Context manager for stacking the current thread-local default
namespace. Exiting the context sets the thread-local default
namespace back to the previously-set namespace. If there is no
previous namespace, then the thread-local namespace is cleared.
Example:
>>>... | Context manager for stacking the current thread-local default
namespace. Exiting the context sets the thread-local default
namespace back to the previously-set namespace. If there is no
previous namespace, then the thread-local namespace is cleared.
Example:
>>> with namespace("foo"):
...... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/namespaces.py#L55-L85 |
Bogdanp/anom-py | anom/model.py | lookup_model_by_kind | def lookup_model_by_kind(kind):
"""Look up the model instance for a given Datastore kind.
Parameters:
kind(str)
Raises:
RuntimeError: If a model for the given kind has not been
defined.
Returns:
model: The model class.
"""
model = _known_models.get(kind)
if model... | python | def lookup_model_by_kind(kind):
"""Look up the model instance for a given Datastore kind.
Parameters:
kind(str)
Raises:
RuntimeError: If a model for the given kind has not been
defined.
Returns:
model: The model class.
"""
model = _known_models.get(kind)
if model... | Look up the model instance for a given Datastore kind.
Parameters:
kind(str)
Raises:
RuntimeError: If a model for the given kind has not been
defined.
Returns:
model: The model class. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L612-L628 |
Bogdanp/anom-py | anom/model.py | delete_multi | def delete_multi(keys):
"""Delete a set of entitites from Datastore by their
respective keys.
Note:
This uses the adapter that is tied to the first model in the list.
If the keys have disparate adapters this function may behave in
unexpected ways.
Warning:
You must pass a **lis... | python | def delete_multi(keys):
"""Delete a set of entitites from Datastore by their
respective keys.
Note:
This uses the adapter that is tied to the first model in the list.
If the keys have disparate adapters this function may behave in
unexpected ways.
Warning:
You must pass a **lis... | Delete a set of entitites from Datastore by their
respective keys.
Note:
This uses the adapter that is tied to the first model in the list.
If the keys have disparate adapters this function may behave in
unexpected ways.
Warning:
You must pass a **list** and not a generator or some... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L631-L673 |
Bogdanp/anom-py | anom/model.py | get_multi | def get_multi(keys):
"""Get a set of entities from Datastore by their respective keys.
Note:
This uses the adapter that is tied to the first model in the
list. If the keys have disparate adapters this function may
behave in unexpected ways.
Warning:
You must pass a **list** and no... | python | def get_multi(keys):
"""Get a set of entities from Datastore by their respective keys.
Note:
This uses the adapter that is tied to the first model in the
list. If the keys have disparate adapters this function may
behave in unexpected ways.
Warning:
You must pass a **list** and no... | Get a set of entities from Datastore by their respective keys.
Note:
This uses the adapter that is tied to the first model in the
list. If the keys have disparate adapters this function may
behave in unexpected ways.
Warning:
You must pass a **list** and not a generator or some other ... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L676-L730 |
Bogdanp/anom-py | anom/model.py | put_multi | def put_multi(entities):
"""Persist a set of entities to Datastore.
Note:
This uses the adapter that is tied to the first Entity in the
list. If the entities have disparate adapters this function may
behave in unexpected ways.
Warning:
You must pass a **list** and not a generator ... | python | def put_multi(entities):
"""Persist a set of entities to Datastore.
Note:
This uses the adapter that is tied to the first Entity in the
list. If the entities have disparate adapters this function may
behave in unexpected ways.
Warning:
You must pass a **list** and not a generator ... | Persist a set of entities to Datastore.
Note:
This uses the adapter that is tied to the first Entity in the
list. If the entities have disparate adapters this function may
behave in unexpected ways.
Warning:
You must pass a **list** and not a generator or some other kind
of iter... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L733-L772 |
Bogdanp/anom-py | anom/model.py | Key.from_path | def from_path(cls, *path, namespace=None):
"""Build up a Datastore key from a path.
Parameters:
\*path(tuple[str or int]): The path segments.
namespace(str): An optional namespace for the key. This is
applied to each key in the tree.
Returns:
anom.Key:... | python | def from_path(cls, *path, namespace=None):
"""Build up a Datastore key from a path.
Parameters:
\*path(tuple[str or int]): The path segments.
namespace(str): An optional namespace for the key. This is
applied to each key in the tree.
Returns:
anom.Key:... | Build up a Datastore key from a path.
Parameters:
\*path(tuple[str or int]): The path segments.
namespace(str): An optional namespace for the key. This is
applied to each key in the tree.
Returns:
anom.Key: The Datastore represented by the given path. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L70-L85 |
Bogdanp/anom-py | anom/model.py | Key.path | def path(self):
"tuple: The full Datastore path represented by this key."
prefix = ()
if self.parent:
prefix = self.parent.path
if self.id_or_name:
return prefix + (self.kind, self.id_or_name)
return prefix + (self.kind,) | python | def path(self):
"tuple: The full Datastore path represented by this key."
prefix = ()
if self.parent:
prefix = self.parent.path
if self.id_or_name:
return prefix + (self.kind, self.id_or_name)
return prefix + (self.kind,) | tuple: The full Datastore path represented by this key. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L88-L97 |
Bogdanp/anom-py | anom/model.py | Key.int_id | def int_id(self):
"int: This key's numeric id."
id_or_name = self.id_or_name
if id_or_name is not None and isinstance(id_or_name, int):
return id_or_name
return None | python | def int_id(self):
"int: This key's numeric id."
id_or_name = self.id_or_name
if id_or_name is not None and isinstance(id_or_name, int):
return id_or_name
return None | int: This key's numeric id. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L105-L110 |
Bogdanp/anom-py | anom/model.py | Key.str_id | def str_id(self):
"str: This key's string id."
id_or_name = self.id_or_name
if id_or_name is not None and isinstance(id_or_name, str):
return id_or_name
return None | python | def str_id(self):
"str: This key's string id."
id_or_name = self.id_or_name
if id_or_name is not None and isinstance(id_or_name, str):
return id_or_name
return None | str: This key's string id. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L113-L118 |
Bogdanp/anom-py | anom/model.py | Property.validate | def validate(self, value):
"""Validates that `value` can be assigned to this Property.
Parameters:
value: The value to validate.
Raises:
TypeError: If the type of the assigned value is invalid.
Returns:
The value that should be assigned to the entity.
... | python | def validate(self, value):
"""Validates that `value` can be assigned to this Property.
Parameters:
value: The value to validate.
Raises:
TypeError: If the type of the assigned value is invalid.
Returns:
The value that should be assigned to the entity.
... | Validates that `value` can be assigned to this Property.
Parameters:
value: The value to validate.
Raises:
TypeError: If the type of the assigned value is invalid.
Returns:
The value that should be assigned to the entity. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L230-L252 |
Bogdanp/anom-py | anom/model.py | Property.prepare_to_store | def prepare_to_store(self, entity, value):
"""Prepare `value` for storage. Called by the Model for each
Property, value pair it contains before handing the data off
to an adapter.
Parameters:
entity(Model): The entity to which the value belongs.
value: The value bei... | python | def prepare_to_store(self, entity, value):
"""Prepare `value` for storage. Called by the Model for each
Property, value pair it contains before handing the data off
to an adapter.
Parameters:
entity(Model): The entity to which the value belongs.
value: The value bei... | Prepare `value` for storage. Called by the Model for each
Property, value pair it contains before handing the data off
to an adapter.
Parameters:
entity(Model): The entity to which the value belongs.
value: The value being stored.
Raises:
RuntimeError: If... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L268-L286 |
Bogdanp/anom-py | anom/model.py | Model.unindexed_properties | def unindexed_properties(self):
"tuple[str]: The names of all the unindexed properties on this entity."
properties = ()
for name, prop in self._properties.items():
if isinstance(prop, EmbedLike):
embedded_entity = getattr(self, name, None)
if embedded_... | python | def unindexed_properties(self):
"tuple[str]: The names of all the unindexed properties on this entity."
properties = ()
for name, prop in self._properties.items():
if isinstance(prop, EmbedLike):
embedded_entity = getattr(self, name, None)
if embedded_... | tuple[str]: The names of all the unindexed properties on this entity. | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L489-L501 |
Bogdanp/anom-py | anom/model.py | Model.get | def get(cls, id_or_name, *, parent=None, namespace=None):
"""Get an entity by id.
Parameters:
id_or_name(int or str): The entity's id.
parent(anom.Key, optional): The entity's parent Key.
namespace(str, optional): The entity's namespace.
Returns:
Model: ... | python | def get(cls, id_or_name, *, parent=None, namespace=None):
"""Get an entity by id.
Parameters:
id_or_name(int or str): The entity's id.
parent(anom.Key, optional): The entity's parent Key.
namespace(str, optional): The entity's namespace.
Returns:
Model: ... | Get an entity by id.
Parameters:
id_or_name(int or str): The entity's id.
parent(anom.Key, optional): The entity's parent Key.
namespace(str, optional): The entity's namespace.
Returns:
Model: An entity or ``None`` if the entity doesn't exist in
Datast... | https://github.com/Bogdanp/anom-py/blob/519078b6d1570fa63c5f17cf98817c7bb5588136/anom/model.py#L519-L531 |
grauwoelfchen/flask-dotenv | flask_dotenv.py | DotEnv.init_app | def init_app(self, app, env_file=None, verbose_mode=False):
"""Imports .env file."""
if self.app is None:
self.app = app
self.verbose_mode = verbose_mode
if env_file is None:
env_file = os.path.join(os.getcwd(), ".env")
if not os.path.exists(env_file):
... | python | def init_app(self, app, env_file=None, verbose_mode=False):
"""Imports .env file."""
if self.app is None:
self.app = app
self.verbose_mode = verbose_mode
if env_file is None:
env_file = os.path.join(os.getcwd(), ".env")
if not os.path.exists(env_file):
... | Imports .env file. | https://github.com/grauwoelfchen/flask-dotenv/blob/7dc811fff18570c4b6803ce48c3ecca7eebabe51/flask_dotenv.py#L24-L35 |
grauwoelfchen/flask-dotenv | flask_dotenv.py | DotEnv.__import_vars | def __import_vars(self, env_file):
"""Actual importing function."""
with open(env_file, "r") as f: # pylint: disable=invalid-name
for line in f:
try:
line = line.lstrip()
if line.startswith('export'):
line = lin... | python | def __import_vars(self, env_file):
"""Actual importing function."""
with open(env_file, "r") as f: # pylint: disable=invalid-name
for line in f:
try:
line = line.lstrip()
if line.startswith('export'):
line = lin... | Actual importing function. | https://github.com/grauwoelfchen/flask-dotenv/blob/7dc811fff18570c4b6803ce48c3ecca7eebabe51/flask_dotenv.py#L37-L60 |
grauwoelfchen/flask-dotenv | flask_dotenv.py | DotEnv.eval | def eval(self, keys):
"""
Examples:
Specify type literal for key.
>>> env.eval({MAIL_PORT: int})
"""
for k, v in keys.items(): # pylint: disable=invalid-name
if k in self.app.config:
try:
val = ast.literal_eval(sel... | python | def eval(self, keys):
"""
Examples:
Specify type literal for key.
>>> env.eval({MAIL_PORT: int})
"""
for k, v in keys.items(): # pylint: disable=invalid-name
if k in self.app.config:
try:
val = ast.literal_eval(sel... | Examples:
Specify type literal for key.
>>> env.eval({MAIL_PORT: int}) | https://github.com/grauwoelfchen/flask-dotenv/blob/7dc811fff18570c4b6803ce48c3ecca7eebabe51/flask_dotenv.py#L62-L86 |
grauwoelfchen/flask-dotenv | flask_dotenv.py | DotEnv.alias | def alias(self, maps):
"""
Examples:
Make alias var -> as.
>>> env.alias(maps={
'TEST_DATABASE_URL': 'SQLALCHEMY_DATABASE_URI',
'TEST_HOST': 'HOST'
})
"""
for k, v in maps.items(): # pylint: disable=invalid-name
... | python | def alias(self, maps):
"""
Examples:
Make alias var -> as.
>>> env.alias(maps={
'TEST_DATABASE_URL': 'SQLALCHEMY_DATABASE_URI',
'TEST_HOST': 'HOST'
})
"""
for k, v in maps.items(): # pylint: disable=invalid-name
... | Examples:
Make alias var -> as.
>>> env.alias(maps={
'TEST_DATABASE_URL': 'SQLALCHEMY_DATABASE_URI',
'TEST_HOST': 'HOST'
}) | https://github.com/grauwoelfchen/flask-dotenv/blob/7dc811fff18570c4b6803ce48c3ecca7eebabe51/flask_dotenv.py#L88-L103 |
jazzband/django-embed-video | docs/ext/djangodocs.py | parse_django_adminopt_node | def parse_django_adminopt_node(env, sig, signode):
"""A copy of sphinx.directives.CmdoptionDesc.parse_signature()"""
from sphinx.domains.std import option_desc_re
count = 0
firstname = ''
for m in option_desc_re.finditer(sig):
optname, args = m.groups()
if count:
signode ... | python | def parse_django_adminopt_node(env, sig, signode):
"""A copy of sphinx.directives.CmdoptionDesc.parse_signature()"""
from sphinx.domains.std import option_desc_re
count = 0
firstname = ''
for m in option_desc_re.finditer(sig):
optname, args = m.groups()
if count:
signode ... | A copy of sphinx.directives.CmdoptionDesc.parse_signature() | https://github.com/jazzband/django-embed-video/blob/6811664c65560840e98ea1db9ff410a359e70681/docs/ext/djangodocs.py#L168-L194 |
Alir3z4/python-stop-words | stop_words/__init__.py | get_stop_words | def get_stop_words(language, cache=True):
"""
:type language: basestring
:rtype: list
"""
try:
language = LANGUAGE_MAPPING[language]
except KeyError:
if language not in AVAILABLE_LANGUAGES:
raise StopWordError('{0}" language is unavailable.'.format(
l... | python | def get_stop_words(language, cache=True):
"""
:type language: basestring
:rtype: list
"""
try:
language = LANGUAGE_MAPPING[language]
except KeyError:
if language not in AVAILABLE_LANGUAGES:
raise StopWordError('{0}" language is unavailable.'.format(
l... | :type language: basestring
:rtype: list | https://github.com/Alir3z4/python-stop-words/blob/7b30f5b953ef02b62dfb4b8a158ea5f1218d11e7/stop_words/__init__.py#L28-L61 |
Alir3z4/python-stop-words | stop_words/__init__.py | apply_filters | def apply_filters(stopwords, language):
"""
Apply registered filters to stopwords
:param stopwords: list
:param language: string
:return: filtered stopwords
"""
if language in _filters:
for func in _filters[language]:
stopwords = func(stopwords)
for func in _filters[... | python | def apply_filters(stopwords, language):
"""
Apply registered filters to stopwords
:param stopwords: list
:param language: string
:return: filtered stopwords
"""
if language in _filters:
for func in _filters[language]:
stopwords = func(stopwords)
for func in _filters[... | Apply registered filters to stopwords
:param stopwords: list
:param language: string
:return: filtered stopwords | https://github.com/Alir3z4/python-stop-words/blob/7b30f5b953ef02b62dfb4b8a158ea5f1218d11e7/stop_words/__init__.py#L66-L80 |
Alir3z4/python-stop-words | stop_words/__init__.py | add_filter | def add_filter(func, language=None):
"""
Register filters for specific language.
If language == None the filter applies for all languages.
Filter will not apply for stop words in cache.
:param func: callable
:param language: string|None
:return:
"""
if language not in _filters:
... | python | def add_filter(func, language=None):
"""
Register filters for specific language.
If language == None the filter applies for all languages.
Filter will not apply for stop words in cache.
:param func: callable
:param language: string|None
:return:
"""
if language not in _filters:
... | Register filters for specific language.
If language == None the filter applies for all languages.
Filter will not apply for stop words in cache.
:param func: callable
:param language: string|None
:return: | https://github.com/Alir3z4/python-stop-words/blob/7b30f5b953ef02b62dfb4b8a158ea5f1218d11e7/stop_words/__init__.py#L83-L94 |
Alir3z4/python-stop-words | stop_words/__init__.py | remove_filter | def remove_filter(func, language=None):
"""
:param func:
:param language:
:return:
"""
if not (language in _filters and func in _filters[language]):
return False
_filters[language].remove(func)
return True | python | def remove_filter(func, language=None):
"""
:param func:
:param language:
:return:
"""
if not (language in _filters and func in _filters[language]):
return False
_filters[language].remove(func)
return True | :param func:
:param language:
:return: | https://github.com/Alir3z4/python-stop-words/blob/7b30f5b953ef02b62dfb4b8a158ea5f1218d11e7/stop_words/__init__.py#L97-L106 |
uktrade/directory-components | directory_components/middleware.py | CountryMiddleware.process_response | def process_response(self, request, response):
"""
Shares config with the language cookie as they serve a similar purpose
"""
if hasattr(request, 'COUNTRY_CODE'):
response.set_cookie(
key=constants.COUNTRY_COOKIE_NAME,
value=request.COUNTRY_CO... | python | def process_response(self, request, response):
"""
Shares config with the language cookie as they serve a similar purpose
"""
if hasattr(request, 'COUNTRY_CODE'):
response.set_cookie(
key=constants.COUNTRY_COOKIE_NAME,
value=request.COUNTRY_CO... | Shares config with the language cookie as they serve a similar purpose | https://github.com/uktrade/directory-components/blob/305b3cfd590e170255503ae3c41aebcaa658af8e/directory_components/middleware.py#L91-L104 |
uktrade/directory-components | directory_components/widgets.py | PrettyIDsMixin.create_option | def create_option(
self, name, value, label, selected, index,
subindex=None, attrs=None):
"""Patch to use nicer ids."""
index = str(index) if subindex is None else "%s%s%s" % (
index, self.id_separator, subindex)
if attrs is None:
attrs = {}
... | python | def create_option(
self, name, value, label, selected, index,
subindex=None, attrs=None):
"""Patch to use nicer ids."""
index = str(index) if subindex is None else "%s%s%s" % (
index, self.id_separator, subindex)
if attrs is None:
attrs = {}
... | Patch to use nicer ids. | https://github.com/uktrade/directory-components/blob/305b3cfd590e170255503ae3c41aebcaa658af8e/directory_components/widgets.py#L15-L47 |
uktrade/directory-components | scripts/upgrade_header_footer.py | current_version | def current_version():
"""Get current version of directory-components."""
filepath = os.path.abspath(
project_root / "directory_components" / "version.py")
version_py = get_file_string(filepath)
regex = re.compile(Utils.get_version)
if regex.search(version_py) is not None:
current_ve... | python | def current_version():
"""Get current version of directory-components."""
filepath = os.path.abspath(
project_root / "directory_components" / "version.py")
version_py = get_file_string(filepath)
regex = re.compile(Utils.get_version)
if regex.search(version_py) is not None:
current_ve... | Get current version of directory-components. | https://github.com/uktrade/directory-components/blob/305b3cfd590e170255503ae3c41aebcaa658af8e/scripts/upgrade_header_footer.py#L27-L42 |
uktrade/directory-components | scripts/upgrade_header_footer.py | get_file_string | def get_file_string(filepath):
"""Get string from file."""
with open(os.path.abspath(filepath)) as f:
return f.read() | python | def get_file_string(filepath):
"""Get string from file."""
with open(os.path.abspath(filepath)) as f:
return f.read() | Get string from file. | https://github.com/uktrade/directory-components/blob/305b3cfd590e170255503ae3c41aebcaa658af8e/scripts/upgrade_header_footer.py#L45-L48 |
uktrade/directory-components | scripts/upgrade_header_footer.py | replace_in_dirs | def replace_in_dirs(version):
"""Look through dirs and run replace_in_files in each."""
print(color(
"Upgrading directory-components dependency in all repos...",
fg='blue', style='bold'))
for dirname in Utils.dirs:
replace = "directory-components=={}".format(version)
replace_... | python | def replace_in_dirs(version):
"""Look through dirs and run replace_in_files in each."""
print(color(
"Upgrading directory-components dependency in all repos...",
fg='blue', style='bold'))
for dirname in Utils.dirs:
replace = "directory-components=={}".format(version)
replace_... | Look through dirs and run replace_in_files in each. | https://github.com/uktrade/directory-components/blob/305b3cfd590e170255503ae3c41aebcaa658af8e/scripts/upgrade_header_footer.py#L59-L67 |
uktrade/directory-components | scripts/upgrade_header_footer.py | replace_in_files | def replace_in_files(dirname, replace):
"""Replace current version with new version in requirements files."""
filepath = os.path.abspath(dirname / "requirements.in")
if os.path.isfile(filepath) and header_footer_exists(filepath):
replaced = re.sub(Utils.exp, replace, get_file_string(filepath))
... | python | def replace_in_files(dirname, replace):
"""Replace current version with new version in requirements files."""
filepath = os.path.abspath(dirname / "requirements.in")
if os.path.isfile(filepath) and header_footer_exists(filepath):
replaced = re.sub(Utils.exp, replace, get_file_string(filepath))
... | Replace current version with new version in requirements files. | https://github.com/uktrade/directory-components/blob/305b3cfd590e170255503ae3c41aebcaa658af8e/scripts/upgrade_header_footer.py#L70-L79 |
uktrade/directory-components | scripts/upgrade_header_footer.py | header_footer_exists | def header_footer_exists(filepath):
"""Check if directory-components is listed in requirements files."""
with open(filepath) as f:
return re.search(Utils.exp, f.read()) | python | def header_footer_exists(filepath):
"""Check if directory-components is listed in requirements files."""
with open(filepath) as f:
return re.search(Utils.exp, f.read()) | Check if directory-components is listed in requirements files. | https://github.com/uktrade/directory-components/blob/305b3cfd590e170255503ae3c41aebcaa658af8e/scripts/upgrade_header_footer.py#L82-L85 |
bxlab/bx-python | lib/bx_extras/pstat.py | abut | def abut (source,*args):
"""
Like the |Stat abut command. It concatenates two lists side-by-side
and returns the result. '2D' lists are also accomodated for either argument
(source or addon). CAUTION: If one list is shorter, it will be repeated
until it is as long as the longest list. If this behavior is not d... | python | def abut (source,*args):
"""
Like the |Stat abut command. It concatenates two lists side-by-side
and returns the result. '2D' lists are also accomodated for either argument
(source or addon). CAUTION: If one list is shorter, it will be repeated
until it is as long as the longest list. If this behavior is not d... | Like the |Stat abut command. It concatenates two lists side-by-side
and returns the result. '2D' lists are also accomodated for either argument
(source or addon). CAUTION: If one list is shorter, it will be repeated
until it is as long as the longest list. If this behavior is not desired,
use pstat.simpleabut().
... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L122-L166 |
bxlab/bx-python | lib/bx_extras/pstat.py | simpleabut | def simpleabut (source, addon):
"""
Concatenates two lists as columns and returns the result. '2D' lists
are also accomodated for either argument (source or addon). This DOES NOT
repeat either list to make the 2 lists of equal length. Beware of list pairs
with different lengths ... the resulting list will be the... | python | def simpleabut (source, addon):
"""
Concatenates two lists as columns and returns the result. '2D' lists
are also accomodated for either argument (source or addon). This DOES NOT
repeat either list to make the 2 lists of equal length. Beware of list pairs
with different lengths ... the resulting list will be the... | Concatenates two lists as columns and returns the result. '2D' lists
are also accomodated for either argument (source or addon). This DOES NOT
repeat either list to make the 2 lists of equal length. Beware of list pairs
with different lengths ... the resulting list will be the length of the
FIRST list passed.
Usage... | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx_extras/pstat.py#L169-L202 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.