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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
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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
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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
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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]]:
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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... | [
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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)
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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,
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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 = {}
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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 | [
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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
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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):
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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:
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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] | [
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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"""
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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):
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- infiles - paths to each input sequence file
- outdirname - path to output directory
- fragsize - the size of sequence fragments
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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
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"""Returns dictionary of sequence fragment lengths, keyed by query name.
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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
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NOTE: ambiguity symbols are not discounted.
"""
fraglengths = {}
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"""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.
"""
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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
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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(
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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(
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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
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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]
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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]
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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
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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
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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
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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.
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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)) | [
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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)
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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 = []
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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.
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sgegroupsize=10000, sgeargs=None):
"""Creates and runs GridEngine scripts for jobs based on the passed
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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
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"""
jobset.add(job)
if len(job.dependencies) == 0:
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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
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"""
# Loop over the job list, creating each job script in turn, and then adding
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widdowquinn/pyani | pyani/run_sge.py | extract_submittable_jobs | def extract_submittable_jobs(waiting):
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- waiting List of Job objects
"""
submittable = set() # Holds jobs that are able to be submitted
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"""Obtain a list of jobs that are able to be submitted from the passed
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widdowquinn/pyani | pyani/run_sge.py | submit_safe_jobs | def submit_safe_jobs(root_dir, jobs, sgeargs=None):
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- root_dir Path to output directory
- jobs Iterable of Job objects
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widdowquinn/pyani | pyani/run_sge.py | submit_jobs | def submit_jobs(root_dir, jobs, sgeargs=None):
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- root_dir Path to output directory
- jobs List of Job objects
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widdowquinn/pyani | pyani/run_sge.py | build_and_submit_jobs | def build_and_submit_jobs(root_dir, jobs, sgeargs=None):
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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(),
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datapythonista/mnist | mnist/__init__.py | download_file | def download_file(fname, target_dir=None, force=False):
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fname : str
Name of the file to download
target_dir : str
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File descriptor of the IDX file to parse
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Byte order of the IDX file. See [1] for available options
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File descriptor of the IDX file to parse
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----------
fname : str
File name to download and parse
target_dir : str
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Bogdanp/anom-py | anom/query.py | Pages.fetch_next_page | def fetch_next_page(self):
"""Fetch the next Page of results.
Returns:
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Returns:
Model: An entity or None if there were no results.
"""
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Model: An entity or None if there were no results.
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Bogdanp/anom-py | anom/namespaces.py | namespace | def namespace(namespace):
"""Context manager for stacking the current thread-local default
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"""Context manager for stacking the current thread-local default
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Bogdanp/anom-py | anom/model.py | lookup_model_by_kind | def lookup_model_by_kind(kind):
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If the keys have disparate adapters this function may behave in
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"""Get a set of entities from Datastore by their respective keys.
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Bogdanp/anom-py | anom/model.py | put_multi | def put_multi(entities):
"""Persist a set of entities to Datastore.
Note:
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Warning:
You must pass a **list** and not a generator ... | python | def put_multi(entities):
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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:
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namespace(str): An optional namespace for the key. This is
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"""Build up a Datastore key from a path.
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\*path(tuple[str or int]): The path segments.
namespace(str): An optional namespace for the key. This is
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Parameters:
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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:
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"""Get an entity by id.
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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.
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grauwoelfchen/flask-dotenv | flask_dotenv.py | DotEnv.init_app | def init_app(self, app, env_file=None, verbose_mode=False):
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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):
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uktrade/directory-components | directory_components/middleware.py | CountryMiddleware.process_response | def process_response(self, request, response):
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uktrade/directory-components | directory_components/widgets.py | PrettyIDsMixin.create_option | def create_option(
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uktrade/directory-components | scripts/upgrade_header_footer.py | current_version | def current_version():
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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_... | [
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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))
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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."""
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"""Check if directory-components is listed in requirements files."""
with open(filepath) as f:
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bxlab/bx-python | lib/bx_extras/pstat.py | linedelimited | def linedelimited (inlist,delimiter):
"""
Returns a string composed of elements in inlist, with each element
separated by 'delimiter.' Used by function writedelimited. Use '\t'
for tab-delimiting.
Usage: linedelimited (inlist,delimiter)
"""
outstr = ''
for item in inlist:
if type(item) != Strin... | python | def linedelimited (inlist,delimiter):
"""
Returns a string composed of elements in inlist, with each element
separated by 'delimiter.' Used by function writedelimited. Use '\t'
for tab-delimiting.
Usage: linedelimited (inlist,delimiter)
"""
outstr = ''
for item in inlist:
if type(item) != Strin... | [
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bxlab/bx-python | lib/bx_extras/pstat.py | lineincustcols | def lineincustcols (inlist,colsizes):
"""
Returns a string composed of elements in inlist, with each element
right-aligned in a column of width specified by a sequence colsizes. The
length of colsizes must be greater than or equal to the number of columns
in inlist.
Usage: lineincustcols (inlist,colsizes)
Retur... | python | def lineincustcols (inlist,colsizes):
"""
Returns a string composed of elements in inlist, with each element
right-aligned in a column of width specified by a sequence colsizes. The
length of colsizes must be greater than or equal to the number of columns
in inlist.
Usage: lineincustcols (inlist,colsizes)
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bxlab/bx-python | lib/bx_extras/pstat.py | list2string | def list2string (inlist,delimit=' '):
"""
Converts a 1D list to a single long string for file output, using
the string.join function.
Usage: list2string (inlist,delimit=' ')
Returns: the string created from inlist
"""
stringlist = [makestr(_) for _ in inlist]
return string.join(stringlist,delimit) | python | def list2string (inlist,delimit=' '):
"""
Converts a 1D list to a single long string for file output, using
the string.join function.
Usage: list2string (inlist,delimit=' ')
Returns: the string created from inlist
"""
stringlist = [makestr(_) for _ in inlist]
return string.join(stringlist,delimit) | [
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bxlab/bx-python | lib/bx_extras/pstat.py | replace | def replace (inlst,oldval,newval):
"""
Replaces all occurrences of 'oldval' with 'newval', recursively.
Usage: replace (inlst,oldval,newval)
"""
lst = inlst*1
for i in range(len(lst)):
if type(lst[i]) not in [ListType,TupleType]:
if lst[i]==oldval: lst[i]=newval
else:
... | python | def replace (inlst,oldval,newval):
"""
Replaces all occurrences of 'oldval' with 'newval', recursively.
Usage: replace (inlst,oldval,newval)
"""
lst = inlst*1
for i in range(len(lst)):
if type(lst[i]) not in [ListType,TupleType]:
if lst[i]==oldval: lst[i]=newval
else:
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bxlab/bx-python | lib/bx_extras/pstat.py | duplicates | def duplicates(inlist):
"""
Returns duplicate items in the FIRST dimension of the passed list.
Usage: duplicates (inlist)
"""
dups = []
for i in range(len(inlist)):
if inlist[i] in inlist[i+1:]:
dups.append(inlist[i])
return dups | python | def duplicates(inlist):
"""
Returns duplicate items in the FIRST dimension of the passed list.
Usage: duplicates (inlist)
"""
dups = []
for i in range(len(inlist)):
if inlist[i] in inlist[i+1:]:
dups.append(inlist[i])
return dups | [
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bxlab/bx-python | lib/bx_extras/pstat.py | nonrepeats | def nonrepeats(inlist):
"""
Returns items that are NOT duplicated in the first dim of the passed list.
Usage: nonrepeats (inlist)
"""
nonrepeats = []
for i in range(len(inlist)):
if inlist.count(inlist[i]) == 1:
nonrepeats.append(inlist[i])
return nonrepeats | python | def nonrepeats(inlist):
"""
Returns items that are NOT duplicated in the first dim of the passed list.
Usage: nonrepeats (inlist)
"""
nonrepeats = []
for i in range(len(inlist)):
if inlist.count(inlist[i]) == 1:
nonrepeats.append(inlist[i])
return nonrepeats | [
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bxlab/bx-python | lib/bx_extras/stats.py | lz | def lz (inlist, score):
"""
Returns the z-score for a given input score, given that score and the
list from which that score came. Not appropriate for population calculations.
Usage: lz(inlist, score)
"""
z = (score-mean(inlist))/samplestdev(inlist)
return z | python | def lz (inlist, score):
"""
Returns the z-score for a given input score, given that score and the
list from which that score came. Not appropriate for population calculations.
Usage: lz(inlist, score)
"""
z = (score-mean(inlist))/samplestdev(inlist)
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bxlab/bx-python | lib/bx_extras/stats.py | llinregress | def llinregress(x,y):
"""
Calculates a regression line on x,y pairs.
Usage: llinregress(x,y) x,y are equal-length lists of x-y coordinates
Returns: slope, intercept, r, two-tailed prob, sterr-of-estimate
"""
TINY = 1.0e-20
if len(x) != len(y):
raise ValueError('Input values not paired in l... | python | def llinregress(x,y):
"""
Calculates a regression line on x,y pairs.
Usage: llinregress(x,y) x,y are equal-length lists of x-y coordinates
Returns: slope, intercept, r, two-tailed prob, sterr-of-estimate
"""
TINY = 1.0e-20
if len(x) != len(y):
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bxlab/bx-python | lib/bx_extras/stats.py | lks_2samp | def lks_2samp (data1,data2):
"""
Computes the Kolmogorov-Smirnof statistic on 2 samples. From
Numerical Recipies in C, page 493.
Usage: lks_2samp(data1,data2) data1&2 are lists of values for 2 conditions
Returns: KS D-value, associated p-value
"""
j1 = 0
j2 = 0
fn1 = 0.0
fn2 = 0.0
n1 = len... | python | def lks_2samp (data1,data2):
"""
Computes the Kolmogorov-Smirnof statistic on 2 samples. From
Numerical Recipies in C, page 493.
Usage: lks_2samp(data1,data2) data1&2 are lists of values for 2 conditions
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j1 = 0
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bxlab/bx-python | lib/bx_extras/stats.py | lranksums | def lranksums(x,y):
"""
Calculates the rank sums statistic on the provided scores and
returns the result. Use only when the n in each condition is > 20 and you
have 2 independent samples of ranks.
Usage: lranksums(x,y)
Returns: a z-statistic, two-tailed p-value
"""
n1 = len(x)
n2 = len(y)
alldata = ... | python | def lranksums(x,y):
"""
Calculates the rank sums statistic on the provided scores and
returns the result. Use only when the n in each condition is > 20 and you
have 2 independent samples of ranks.
Usage: lranksums(x,y)
Returns: a z-statistic, two-tailed p-value
"""
n1 = len(x)
n2 = len(y)
alldata = ... | [
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bxlab/bx-python | lib/bx_extras/stats.py | lkruskalwallish | def lkruskalwallish(*args):
"""
The Kruskal-Wallis H-test is a non-parametric ANOVA for 3 or more
groups, requiring at least 5 subjects in each group. This function
calculates the Kruskal-Wallis H-test for 3 or more independent samples
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Usage: lkruskalwallish(*args)
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"""
The Kruskal-Wallis H-test is a non-parametric ANOVA for 3 or more
groups, requiring at least 5 subjects in each group. This function
calculates the Kruskal-Wallis H-test for 3 or more independent samples
and returns the result.
Usage: lkruskalwallish(*args)
Returns: H-statistic... | [
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bxlab/bx-python | lib/bx_extras/stats.py | lksprob | def lksprob(alam):
"""
Computes a Kolmolgorov-Smirnov t-test significance level. Adapted from
Numerical Recipies.
Usage: lksprob(alam)
"""
fac = 2.0
sum = 0.0
termbf = 0.0
a2 = -2.0*alam*alam
for j in range(1,201):
term = fac*math.exp(a2*j*j)
sum = sum + term
if math.... | python | def lksprob(alam):
"""
Computes a Kolmolgorov-Smirnov t-test significance level. Adapted from
Numerical Recipies.
Usage: lksprob(alam)
"""
fac = 2.0
sum = 0.0
termbf = 0.0
a2 = -2.0*alam*alam
for j in range(1,201):
term = fac*math.exp(a2*j*j)
sum = sum + term
if math.... | [
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bxlab/bx-python | lib/bx_extras/stats.py | outputpairedstats | def outputpairedstats(fname,writemode,name1,n1,m1,se1,min1,max1,name2,n2,m2,se2,min2,max2,statname,stat,prob):
"""
Prints or write to a file stats for two groups, using the name, n,
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Usage: outputpaireds... | python | def outputpairedstats(fname,writemode,name1,n1,m1,se1,min1,max1,name2,n2,m2,se2,min2,max2,statname,stat,prob):
"""
Prints or write to a file stats for two groups, using the name, n,
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its value, and the associated p-value.
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bxlab/bx-python | lib/bx/gene_reader.py | GeneReader | def GeneReader( fh, format='gff' ):
""" yield chrom, strand, gene_exons, name """
known_formats = ( 'gff', 'gtf', 'bed')
if format not in known_formats:
print('%s format not in %s' % (format, ",".join( known_formats )), file=sys.stderr)
raise Exception('?')
if format == 'bed':
... | python | def GeneReader( fh, format='gff' ):
""" yield chrom, strand, gene_exons, name """
known_formats = ( 'gff', 'gtf', 'bed')
if format not in known_formats:
print('%s format not in %s' % (format, ",".join( known_formats )), file=sys.stderr)
raise Exception('?')
if format == 'bed':
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bxlab/bx-python | lib/bx/seq/seq.py | SeqFile.get | def get(self, start, length):
"""
Fetch subsequence starting at position `start` with length `length`.
This method is picky about parameters, the requested interval must
have non-negative length and fit entirely inside the NIB sequence,
the returned string will contain exactly ... | python | def get(self, start, length):
"""
Fetch subsequence starting at position `start` with length `length`.
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bxlab/bx-python | lib/bx/align/score.py | read_scoring_scheme | def read_scoring_scheme( f, gap_open, gap_extend, gap1="-", gap2=None, **kwargs ):
"""
Initialize scoring scheme from a file containint a blastz style text blob.
f can be either a file or the name of a file.
"""
close_it = False
if (type(f) == str):
f = file(f,"rt")
close_it = Tr... | python | def read_scoring_scheme( f, gap_open, gap_extend, gap1="-", gap2=None, **kwargs ):
"""
Initialize scoring scheme from a file containint a blastz style text blob.
f can be either a file or the name of a file.
"""
close_it = False
if (type(f) == str):
f = file(f,"rt")
close_it = Tr... | [
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bxlab/bx-python | lib/bx/align/core.py | shuffle_columns | def shuffle_columns( a ):
"""Randomize the columns of an alignment"""
mask = range( a.text_size )
random.shuffle( mask )
for c in a.components:
c.text = ''.join( [ c.text[i] for i in mask ] ) | python | def shuffle_columns( a ):
"""Randomize the columns of an alignment"""
mask = range( a.text_size )
random.shuffle( mask )
for c in a.components:
c.text = ''.join( [ c.text[i] for i in mask ] ) | [
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bxlab/bx-python | lib/bx/align/core.py | Alignment.slice_by_component | def slice_by_component( self, component_index, start, end ):
"""
Return a slice of the alignment, corresponding to an coordinate interval in a specific component.
component_index is one of
an integer offset into the components list
a string indicating the src of the desi... | python | def slice_by_component( self, component_index, start, end ):
"""
Return a slice of the alignment, corresponding to an coordinate interval in a specific component.
component_index is one of
an integer offset into the components list
a string indicating the src of the desi... | [
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bxlab/bx-python | lib/bx/align/core.py | Alignment.remove_all_gap_columns | def remove_all_gap_columns( self ):
"""
Remove any columns containing only gaps from alignment components,
text of components is modified IN PLACE.
"""
seqs = []
for c in self.components:
try:
seqs.append( list( c.text ) )
except Ty... | python | def remove_all_gap_columns( self ):
"""
Remove any columns containing only gaps from alignment components,
text of components is modified IN PLACE.
"""
seqs = []
for c in self.components:
try:
seqs.append( list( c.text ) )
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bxlab/bx-python | lib/bx/align/core.py | Component.slice_by_coord | def slice_by_coord( self, start, end ):
"""
Return the slice of the component corresponding to a coordinate interval.
start and end are relative to the + strand, regardless of the component's strand.
"""
start_col = self.coord_to_col( start )
end_col = self.coord_to_col... | python | def slice_by_coord( self, start, end ):
"""
Return the slice of the component corresponding to a coordinate interval.
start and end are relative to the + strand, regardless of the component's strand.
"""
start_col = self.coord_to_col( start )
end_col = self.coord_to_col... | [
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bxlab/bx-python | lib/bx/align/core.py | Component.coord_to_col | def coord_to_col( self, pos ):
"""
Return the alignment column index corresponding to coordinate pos.
pos is relative to the + strand, regardless of the component's strand.
"""
start,end = self.get_forward_strand_start(),self.get_forward_strand_end()
if pos < start or p... | python | def coord_to_col( self, pos ):
"""
Return the alignment column index corresponding to coordinate pos.
pos is relative to the + strand, regardless of the component's strand.
"""
start,end = self.get_forward_strand_start(),self.get_forward_strand_end()
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bxlab/bx-python | lib/bx/align/tools/thread.py | get_components_for_species | def get_components_for_species( alignment, species ):
"""Return the component for each species in the list `species` or None"""
# If the number of components in the alignment is less that the requested number
# of species we can immediately fail
if len( alignment.components ) < len( species ): return No... | python | def get_components_for_species( alignment, species ):
"""Return the component for each species in the list `species` or None"""
# If the number of components in the alignment is less that the requested number
# of species we can immediately fail
if len( alignment.components ) < len( species ): return No... | [
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bxlab/bx-python | lib/bx/align/maf.py | read_next_maf | def read_next_maf( file, species_to_lengths=None, parse_e_rows=False ):
"""
Read the next MAF block from `file` and return as an `Alignment`
instance. If `parse_i_rows` is true, empty components will be created
when e rows are encountered.
"""
alignment = Alignment(species_to_lengths=species_t... | python | def read_next_maf( file, species_to_lengths=None, parse_e_rows=False ):
"""
Read the next MAF block from `file` and return as an `Alignment`
instance. If `parse_i_rows` is true, empty components will be created
when e rows are encountered.
"""
alignment = Alignment(species_to_lengths=species_t... | [
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bxlab/bx-python | lib/bx/align/maf.py | readline | def readline( file, skip_blank=False ):
"""Read a line from provided file, skipping any blank or comment lines"""
while 1:
line = file.readline()
#print "every line: %r" % line
if not line: return None
if line[0] != '#' and not ( skip_blank and line.isspace() ):
retu... | python | def readline( file, skip_blank=False ):
"""Read a line from provided file, skipping any blank or comment lines"""
while 1:
line = file.readline()
#print "every line: %r" % line
if not line: return None
if line[0] != '#' and not ( skip_blank and line.isspace() ):
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] | 09cb725284803df90a468d910f2274628d8647de | https://github.com/bxlab/bx-python/blob/09cb725284803df90a468d910f2274628d8647de/lib/bx/align/maf.py#L203-L210 | train |
bxlab/bx-python | lib/bx/align/maf.py | parse_attributes | def parse_attributes( fields ):
"""Parse list of key=value strings into a dict"""
attributes = {}
for field in fields:
pair = field.split( '=' )
attributes[ pair[0] ] = pair[1]
return attributes | python | def parse_attributes( fields ):
"""Parse list of key=value strings into a dict"""
attributes = {}
for field in fields:
pair = field.split( '=' )
attributes[ pair[0] ] = pair[1]
return attributes | [
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bxlab/bx-python | lib/bx/motif/io/transfac.py | TransfacReader.as_dict | def as_dict( self, key="id" ):
"""
Return a dictionary containing all remaining motifs, using `key`
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"""
rval = {}
for motif in self:
rval[ getattr( motif, key ) ] = motif
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"""
Return a dictionary containing all remaining motifs, using `key`
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"""
rval = {}
for motif in self:
rval[ getattr( motif, key ) ] = motif
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bxlab/bx-python | lib/bx/motif/io/transfac.py | TransfacReader.parse_record | def parse_record( self, lines ):
"""
Parse a TRANSFAC record out of `lines` and return a motif.
"""
# Break lines up
temp_lines = []
for line in lines:
fields = line.rstrip( "\r\n" ).split( None, 1 )
if len( fields ) == 1:
fields.ap... | python | def parse_record( self, lines ):
"""
Parse a TRANSFAC record out of `lines` and return a motif.
"""
# Break lines up
temp_lines = []
for line in lines:
fields = line.rstrip( "\r\n" ).split( None, 1 )
if len( fields ) == 1:
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bxlab/bx-python | scripts/bed_rand_intersect.py | bit_clone | def bit_clone( bits ):
"""
Clone a bitset
"""
new = BitSet( bits.size )
new.ior( bits )
return new | python | def bit_clone( bits ):
"""
Clone a bitset
"""
new = BitSet( bits.size )
new.ior( bits )
return new | [
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bxlab/bx-python | scripts/bed_rand_intersect.py | throw_random | def throw_random( lengths, mask ):
"""
Try multiple times to run 'throw_random'
"""
saved = None
for i in range( maxtries ):
try:
return throw_random_bits( lengths, mask )
except MaxtriesException as e:
saved = e
continue
raise e | python | def throw_random( lengths, mask ):
"""
Try multiple times to run 'throw_random'
"""
saved = None
for i in range( maxtries ):
try:
return throw_random_bits( lengths, mask )
except MaxtriesException as e:
saved = e
continue
raise e | [
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bxlab/bx-python | scripts/bed_rand_intersect.py | as_bits | def as_bits( region_start, region_length, intervals ):
"""
Convert a set of intervals overlapping a region of a chromosome into
a bitset for just that region with the bits covered by the intervals
set.
"""
bits = BitSet( region_length )
for chr, start, stop in intervals:
bits.set_r... | python | def as_bits( region_start, region_length, intervals ):
"""
Convert a set of intervals overlapping a region of a chromosome into
a bitset for just that region with the bits covered by the intervals
set.
"""
bits = BitSet( region_length )
for chr, start, stop in intervals:
bits.set_r... | [
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bxlab/bx-python | scripts/bed_rand_intersect.py | interval_lengths | def interval_lengths( bits ):
"""
Get the length distribution of all contiguous runs of set bits from
"""
end = 0
while 1:
start = bits.next_set( end )
if start == bits.size: break
end = bits.next_clear( start )
yield end - start | python | def interval_lengths( bits ):
"""
Get the length distribution of all contiguous runs of set bits from
"""
end = 0
while 1:
start = bits.next_set( end )
if start == bits.size: break
end = bits.next_clear( start )
yield end - start | [
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bxlab/bx-python | scripts/bed_rand_intersect.py | count_overlap | def count_overlap( bits1, bits2 ):
"""
Count the number of bits that overlap between two sets
"""
b = BitSet( bits1.size )
b |= bits1
b &= bits2
return b.count_range( 0, b.size ) | python | def count_overlap( bits1, bits2 ):
"""
Count the number of bits that overlap between two sets
"""
b = BitSet( bits1.size )
b |= bits1
b &= bits2
return b.count_range( 0, b.size ) | [
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bxlab/bx-python | scripts/bed_rand_intersect.py | overlapping_in_bed | def overlapping_in_bed( fname, r_chr, r_start, r_stop ):
"""
Get from a bed all intervals that overlap the region defined by
r_chr, r_start, r_stop.
"""
rval = []
for line in open( fname ):
if line.startswith( "#" ) or line.startswith( "track" ):
continue
fields = lin... | python | def overlapping_in_bed( fname, r_chr, r_start, r_stop ):
"""
Get from a bed all intervals that overlap the region defined by
r_chr, r_start, r_stop.
"""
rval = []
for line in open( fname ):
if line.startswith( "#" ) or line.startswith( "track" ):
continue
fields = lin... | [
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bxlab/bx-python | lib/bx/align/tools/tile.py | tile_interval | def tile_interval( sources, index, ref_src, start, end, seq_db=None ):
"""
Tile maf blocks onto an interval. The resulting block will span the interval
exactly and contain the column from the highest scoring alignment at each
position.
`sources`: list of sequence source names to include in final bl... | python | def tile_interval( sources, index, ref_src, start, end, seq_db=None ):
"""
Tile maf blocks onto an interval. The resulting block will span the interval
exactly and contain the column from the highest scoring alignment at each
position.
`sources`: list of sequence source names to include in final bl... | [
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`index`: an instnace that can return maf blocks overlapping intervals
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bxlab/bx-python | scripts/maf_tile_2bit.py | get_fill_char | def get_fill_char( maf_status ):
"""
Return the character that should be used to fill between blocks
having a given status
"""
## assert maf_status not in ( maf.MAF_CONTIG_NESTED_STATUS, maf.MAF_NEW_NESTED_STATUS,
## maf.MAF_MAYBE_NEW_NESTED_STATUS ), \
## "Ne... | python | def get_fill_char( maf_status ):
"""
Return the character that should be used to fill between blocks
having a given status
"""
## assert maf_status not in ( maf.MAF_CONTIG_NESTED_STATUS, maf.MAF_NEW_NESTED_STATUS,
## maf.MAF_MAYBE_NEW_NESTED_STATUS ), \
## "Ne... | [
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bxlab/bx-python | scripts/maf_tile_2bit.py | guess_fill_char | def guess_fill_char( left_comp, right_comp ):
"""
For the case where there is no annotated synteny we will try to guess it
"""
# No left component, obiously new
return "*"
# First check that the blocks have the same src (not just species) and
# orientation
if ( left_comp.src == right_co... | python | def guess_fill_char( left_comp, right_comp ):
"""
For the case where there is no annotated synteny we will try to guess it
"""
# No left component, obiously new
return "*"
# First check that the blocks have the same src (not just species) and
# orientation
if ( left_comp.src == right_co... | [
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bxlab/bx-python | scripts/maf_tile_2bit.py | remove_all_gap_columns | def remove_all_gap_columns( texts ):
"""
Remove any columns containing only gaps from alignment texts
"""
seqs = [ list( t ) for t in texts ]
i = 0
text_size = len( texts[0] )
while i < text_size:
all_gap = True
for seq in seqs:
if seq[i] not in ( '-', '#', '*', '... | python | def remove_all_gap_columns( texts ):
"""
Remove any columns containing only gaps from alignment texts
"""
seqs = [ list( t ) for t in texts ]
i = 0
text_size = len( texts[0] )
while i < text_size:
all_gap = True
for seq in seqs:
if seq[i] not in ( '-', '#', '*', '... | [
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bxlab/bx-python | lib/bx/cookbook/__init__.py | cross_lists | def cross_lists(*sets):
"""Return the cross product of the arguments"""
wheels = [iter(_) for _ in sets]
digits = [next(it) for it in wheels]
while True:
yield digits[:]
for i in range(len(digits)-1, -1, -1):
try:
digits[i] = next(wheels[i])
br... | python | def cross_lists(*sets):
"""Return the cross product of the arguments"""
wheels = [iter(_) for _ in sets]
digits = [next(it) for it in wheels]
while True:
yield digits[:]
for i in range(len(digits)-1, -1, -1):
try:
digits[i] = next(wheels[i])
br... | [
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