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flo-compbio/genometools | genometools/basic/gene_set.py | GeneSet.from_list | def from_list(cls, l):
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Note: See also :meth:`to_list`.
Parameters
----------
l: list or tuple of str
A list of strings representing gene set ID, name, genes,
source, collection, and description. The g... | python | def from_list(cls, l):
"""Generate an GeneSet object from a list of strings.
Note: See also :meth:`to_list`.
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acorg/dark-matter | dark/sequence.py | findPrimer | def findPrimer(primer, seq):
"""
Look for a primer sequence.
@param primer: A C{str} primer sequence.
@param seq: A BioPython C{Bio.Seq} sequence.
@return: A C{list} of zero-based offsets into the sequence at which the
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... | python | def findPrimer(primer, seq):
"""
Look for a primer sequence.
@param primer: A C{str} primer sequence.
@param seq: A BioPython C{Bio.Seq} sequence.
@return: A C{list} of zero-based offsets into the sequence at which the
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acorg/dark-matter | dark/sequence.py | findPrimerBidi | def findPrimerBidi(primer, seq):
"""
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@param primer: A C{str} primer sequence.
@param seq: A BioPython C{Bio.Seq} sequence.
@return: A C{tuple} of two lists. The first contains (zero-based)
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"""
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acorg/dark-matter | dark/sequence.py | findPrimerBidiLimits | def findPrimerBidiLimits(primer, seq):
"""
Report the extreme (inner) offsets of primer in a sequence and its
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@param primer: A C{str} primer sequence.
@param seq: A BioPython C{Bio.Seq} sequence.
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"""
Report the extreme (inner) offsets of primer in a sequence and its
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@param primer: A C{str} primer sequence.
@param seq: A BioPython C{Bio.Seq} sequence.
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acorg/dark-matter | dark/utils.py | numericallySortFilenames | def numericallySortFilenames(names):
"""
Sort (ascending) a list of file names by their numerical prefixes.
The number sorted on is the numeric prefix of the basename of
the given filename. E.g., '../output/1.json.bz2' will sort before
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"""
Sort (ascending) a list of file names by their numerical prefixes.
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acorg/dark-matter | dark/utils.py | asHandle | def asHandle(fileNameOrHandle, mode='r'):
"""
Decorator for file opening that makes it easy to open compressed files.
Based on L{Bio.File.as_handle}.
@param fileNameOrHandle: Either a C{str} or a file handle.
@return: A generator that can be turned into a context manager via
L{contextlib.co... | python | def asHandle(fileNameOrHandle, mode='r'):
"""
Decorator for file opening that makes it easy to open compressed files.
Based on L{Bio.File.as_handle}.
@param fileNameOrHandle: Either a C{str} or a file handle.
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acorg/dark-matter | dark/utils.py | parseRangeString | def parseRangeString(s, convertToZeroBased=False):
"""
Parse a range string of the form 1-5,12,100-200.
@param s: A C{str} specifiying a set of numbers, given in the form of
comma separated numeric ranges or individual indices.
@param convertToZeroBased: If C{True} all indices will have one
... | python | def parseRangeString(s, convertToZeroBased=False):
"""
Parse a range string of the form 1-5,12,100-200.
@param s: A C{str} specifiying a set of numbers, given in the form of
comma separated numeric ranges or individual indices.
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acorg/dark-matter | dark/utils.py | nucleotidesToStr | def nucleotidesToStr(nucleotides, prefix=''):
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@param nucleotides: A C{defaultdict(Counter)} instance, keyed
by C{int} offset, with nucleotides keying the Counters.
@param prefix: A C{str} to put at the start of each line.
@return: A C{str} re... | python | def nucleotidesToStr(nucleotides, prefix=''):
"""
Convert offsets and base counts to a string.
@param nucleotides: A C{defaultdict(Counter)} instance, keyed
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acorg/dark-matter | dark/utils.py | countPrint | def countPrint(mesg, count, len1, len2=None):
"""
Format a message followed by an integer count and a percentage (or
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@param mesg: a C{str} message.
@param count: a numeric value.
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@param len2: the C{int}... | python | def countPrint(mesg, count, len1, len2=None):
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Format a message followed by an integer count and a percentage (or
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@param mesg: a C{str} message.
@param count: a numeric value.
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flo-compbio/genometools | genometools/gcloud/tasks/util.py | upload_scripts | def upload_scripts(client, script_dir, overwrite=True):
"""Uploads general-purpose scripts to a Google Storage bucket.
TODO: docstring"""
local_dir = os.path.join(genometools._root, 'data', 'gcloud', 'scripts')
match = _BUCKET_PAT.match(script_dir)
script_bucket = match.group(1)
script_pref... | python | def upload_scripts(client, script_dir, overwrite=True):
"""Uploads general-purpose scripts to a Google Storage bucket.
TODO: docstring"""
local_dir = os.path.join(genometools._root, 'data', 'gcloud', 'scripts')
match = _BUCKET_PAT.match(script_dir)
script_bucket = match.group(1)
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acorg/dark-matter | dark/diamond/alignments.py | DiamondReadsAlignments._getReader | def _getReader(self, filename, scoreClass):
"""
Obtain a JSON record reader for DIAMOND records.
@param filename: The C{str} file name holding the JSON.
@param scoreClass: A class to hold and compare scores (see scores.py).
"""
if filename.endswith('.json') or filename.e... | python | def _getReader(self, filename, scoreClass):
"""
Obtain a JSON record reader for DIAMOND records.
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acorg/dark-matter | dark/diamond/alignments.py | DiamondReadsAlignments.iter | def iter(self):
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acorg/dark-matter | dark/diamond/alignments.py | DiamondReadsAlignments.getSubjectSequence | def getSubjectSequence(self, title):
"""
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@raise KeyError: If the C{title} is not present in the DIAMOND
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flo-compbio/genometools | genometools/ncbi/sra/util.py | get_project_urls | def get_project_urls(project):
"""Get the URLs for all runs from a given project.
TODO: docstring"""
urls = []
with ftputil.FTPHost(sra_host, sra_user, sra_password) as ftp_host:
download_paths = []
exp_dir = '/sra/sra-instant/reads/ByStudy/sra/SRP/%s/%s/' \
%(projec... | python | def get_project_urls(project):
"""Get the URLs for all runs from a given project.
TODO: docstring"""
urls = []
with ftputil.FTPHost(sra_host, sra_user, sra_password) as ftp_host:
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nkavaldj/myhdl_lib | examples/pipeline_control_simple.py | twos_complement | def twos_complement(rst, clk, rx_rdy, rx_vld, rx_dat, tx_rdy, tx_vld, tx_dat):
''' Two's complement conversion of a binary number
Input handshake & data
rx_rdy - (o) Ready
rx_vld - (i) Valid
rx_dat - (i) Data
Output handshake & data
tx_rdy - (i) Ready
... | python | def twos_complement(rst, clk, rx_rdy, rx_vld, rx_dat, tx_rdy, tx_vld, tx_dat):
''' Two's complement conversion of a binary number
Input handshake & data
rx_rdy - (o) Ready
rx_vld - (i) Valid
rx_dat - (i) Data
Output handshake & data
tx_rdy - (i) Ready
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flo-compbio/genometools | genometools/ncbi/extract_entrez2gene.py | get_argument_parser | def get_argument_parser():
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flo-compbio/genometools | genometools/ncbi/extract_entrez2gene.py | read_gene2acc | def read_gene2acc(file_path, logger):
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Parameters
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file_path: str
The path of the gene2accession.gz file (or a filtered version thereof).
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file_path: str
The path of the gene2accession.gz file (or a filtered version thereof).
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flo-compbio/genometools | genometools/ncbi/extract_entrez2gene.py | write_entrez2gene | def write_entrez2gene(file_path, entrez2gene, logger):
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flo-compbio/genometools | genometools/ncbi/extract_entrez2gene.py | main | def main(args=None):
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acorg/dark-matter | dark/aa.py | find | def find(s):
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Find an amino acid whose name or abbreviation is s.
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"""
Find an amino acid whose name or abbreviation is s.
@param s: A C{str} amino acid specifier. This may be a full name,
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Extract amino acid property values or cluster numbers for a sequence.
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@param read1: A C{Read} instance or an instance of one of its subclasses.
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"""
Format amino acid sequence match as a string.
@param aaMatch: A C{dict} returned by C{compareAaReads}.
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acorg/dark-matter | dark/aa.py | compareAaReads | def compareAaReads(read1, read2, gapChars='-', offsets=None):
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@param read1: A C{Read} instance or an instance of one of its subclasses.
@param read2: A C{Read} instance or an instance of one of its subclasses.
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"""
Compare two amino acid sequences.
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acorg/dark-matter | bin/noninteractive-alignment-panel.py | parseColors | def parseColors(colors, args):
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Parse read id color specification.
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"""
Parse read id color specification.
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flo-compbio/genometools | genometools/ontology/util.py | download_release | def download_release(download_file, release=None):
"""Downloads the "go-basic.obo" file for the specified release."""
if release is None:
release = get_latest_release()
url = 'http://viewvc.geneontology.org/viewvc/GO-SVN/ontology-releases/%s/go-basic.obo' % release
#download_file = 'go-basic_%s.... | python | def download_release(download_file, release=None):
"""Downloads the "go-basic.obo" file for the specified release."""
if release is None:
release = get_latest_release()
url = 'http://viewvc.geneontology.org/viewvc/GO-SVN/ontology-releases/%s/go-basic.obo' % release
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flo-compbio/genometools | genometools/ontology/util.py | get_current_ontology_date | def get_current_ontology_date():
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invenia/Arbiter | arbiter/sync.py | execute | def execute(function, name):
"""
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"""
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except Exception as exc:
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disqus/overseer | overseer/templatetags/overseer_helpers.py | truncatechars | def truncatechars(value, arg):
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Truncates a string after a certain number of chars.
Argument: Number of chars to truncate after.
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try:
length = int(arg)
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Truncates a string after a certain number of chars.
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disqus/overseer | example_project/urls.py | handler500 | def handler500(request):
"""
500 error handler.
Templates: `500.html`
Context: None
"""
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from django.http import HttpResponseServerError
from overseer.context_processors import default
import logging
import sys
try:
context ... | python | def handler500(request):
"""
500 error handler.
Templates: `500.html`
Context: None
"""
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from django.http import HttpResponseServerError
from overseer.context_processors import default
import logging
import sys
try:
context ... | [
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Templates: `500.html`
Context: None | [
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flo-compbio/genometools | genometools/ensembl/cli/util.py | get_gtf_argument_parser | def get_gtf_argument_parser(desc, default_field_name='gene'):
"""Return an argument parser with basic options for reading GTF files.
Parameters
----------
desc: str
Description of the ArgumentParser
default_field_name: str, optional
Name of field in GTF file to look for.
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"""Return an argument parser with basic options for reading GTF files.
Parameters
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desc: str
Description of the ArgumentParser
default_field_name: str, optional
Name of field in GTF file to look for.
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inveniosoftware/invenio-jsonschemas | invenio_jsonschemas/jsonresolver.py | jsonresolver_loader | def jsonresolver_loader(url_map):
"""JSON resolver plugin that loads the schema endpoint.
Injected into Invenio-Records JSON resolver.
"""
from flask import current_app
from . import current_jsonschemas
url_map.add(Rule(
"{0}/<path:path>".format(current_app.config['JSONSCHEMAS_ENDPOINT'... | python | def jsonresolver_loader(url_map):
"""JSON resolver plugin that loads the schema endpoint.
Injected into Invenio-Records JSON resolver.
"""
from flask import current_app
from . import current_jsonschemas
url_map.add(Rule(
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grabbles/grabbit | grabbit/core.py | merge_layouts | def merge_layouts(layouts):
''' Utility function for merging multiple layouts.
Args:
layouts (list): A list of BIDSLayout instances to merge.
Returns:
A BIDSLayout containing merged files and entities.
Notes:
Layouts will be merged in the order of the elements in the list. I.e.,... | python | def merge_layouts(layouts):
''' Utility function for merging multiple layouts.
Args:
layouts (list): A list of BIDSLayout instances to merge.
Returns:
A BIDSLayout containing merged files and entities.
Notes:
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grabbles/grabbit | grabbit/core.py | File._matches | def _matches(self, entities=None, extensions=None, domains=None,
regex_search=False):
"""
Checks whether the file matches all of the passed entities and
extensions.
Args:
entities (dict): A dictionary of entity names -> regex patterns.
extensions... | python | def _matches(self, entities=None, extensions=None, domains=None,
regex_search=False):
"""
Checks whether the file matches all of the passed entities and
extensions.
Args:
entities (dict): A dictionary of entity names -> regex patterns.
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grabbles/grabbit | grabbit/core.py | File.as_named_tuple | def as_named_tuple(self):
"""
Returns the File as a named tuple. The full path plus all entity
key/value pairs are returned as attributes.
"""
keys = list(self.entities.keys())
replaced = []
for i, k in enumerate(keys):
if iskeyword(k):
... | python | def as_named_tuple(self):
"""
Returns the File as a named tuple. The full path plus all entity
key/value pairs are returned as attributes.
"""
keys = list(self.entities.keys())
replaced = []
for i, k in enumerate(keys):
if iskeyword(k):
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grabbles/grabbit | grabbit/core.py | File.copy | def copy(self, path_patterns, symbolic_link=False, root=None,
conflicts='fail'):
''' Copy the contents of a file to a new location, with target
filename defined by the current File's entities and the specified
path_patterns. '''
new_filename = build_path(self.entities, path_... | python | def copy(self, path_patterns, symbolic_link=False, root=None,
conflicts='fail'):
''' Copy the contents of a file to a new location, with target
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grabbles/grabbit | grabbit/core.py | Entity.match_file | def match_file(self, f, update_file=False):
"""
Determine whether the passed file matches the Entity.
Args:
f (File): The File instance to match against.
Returns: the matched value if a match was found, otherwise None.
"""
if self.map_func is not None:
... | python | def match_file(self, f, update_file=False):
"""
Determine whether the passed file matches the Entity.
Args:
f (File): The File instance to match against.
Returns: the matched value if a match was found, otherwise None.
"""
if self.map_func is not None:
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grabbles/grabbit | grabbit/core.py | Layout._get_or_load_domain | def _get_or_load_domain(self, domain):
''' Return a domain if one already exists, or create a new one if not.
Args:
domain (str, dict): Can be one of:
- The name of the Domain to return (fails if none exists)
- A path to the Domain configuration file
... | python | def _get_or_load_domain(self, domain):
''' Return a domain if one already exists, or create a new one if not.
Args:
domain (str, dict): Can be one of:
- The name of the Domain to return (fails if none exists)
- A path to the Domain configuration file
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grabbles/grabbit | grabbit/core.py | Layout._check_inclusions | def _check_inclusions(self, f, domains=None):
''' Check file or directory against regexes in config to determine if
it should be included in the index '''
filename = f if isinstance(f, six.string_types) else f.path
if domains is None:
domains = list(self.domains.values(... | python | def _check_inclusions(self, f, domains=None):
''' Check file or directory against regexes in config to determine if
it should be included in the index '''
filename = f if isinstance(f, six.string_types) else f.path
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grabbles/grabbit | grabbit/core.py | Layout._find_entity | def _find_entity(self, entity):
''' Find an Entity instance by name. Checks both name and id fields.'''
if entity in self.entities:
return self.entities[entity]
_ent = [e for e in self.entities.values() if e.name == entity]
if len(_ent) > 1:
raise ValueError("Enti... | python | def _find_entity(self, entity):
''' Find an Entity instance by name. Checks both name and id fields.'''
if entity in self.entities:
return self.entities[entity]
_ent = [e for e in self.entities.values() if e.name == entity]
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grabbles/grabbit | grabbit/core.py | Layout.save_index | def save_index(self, filename):
''' Save the current Layout's index to a .json file.
Args:
filename (str): Filename to write to.
Note: At the moment, this won't serialize directory-specific config
files. This means reconstructed indexes will only work properly in
ca... | python | def save_index(self, filename):
''' Save the current Layout's index to a .json file.
Args:
filename (str): Filename to write to.
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grabbles/grabbit | grabbit/core.py | Layout.load_index | def load_index(self, filename, reindex=False):
''' Load the Layout's index from a plaintext file.
Args:
filename (str): Path to the plaintext index file.
reindex (bool): If True, discards entity values provided in the
loaded index and instead re-indexes every fil... | python | def load_index(self, filename, reindex=False):
''' Load the Layout's index from a plaintext file.
Args:
filename (str): Path to the plaintext index file.
reindex (bool): If True, discards entity values provided in the
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grabbles/grabbit | grabbit/core.py | Layout.add_entity | def add_entity(self, domain, **kwargs):
''' Add a new Entity to tracking. '''
# Set the entity's mapping func if one was specified
map_func = kwargs.get('map_func', None)
if map_func is not None and not callable(kwargs['map_func']):
if self.entity_mapper is None:
... | python | def add_entity(self, domain, **kwargs):
''' Add a new Entity to tracking. '''
# Set the entity's mapping func if one was specified
map_func = kwargs.get('map_func', None)
if map_func is not None and not callable(kwargs['map_func']):
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grabbles/grabbit | grabbit/core.py | Layout.get | def get(self, return_type='tuple', target=None, extensions=None,
domains=None, regex_search=None, **kwargs):
"""
Retrieve files and/or metadata from the current Layout.
Args:
return_type (str): Type of result to return. Valid values:
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"""
Retrieve files and/or metadata from the current Layout.
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return_type (str): Type of result to return. Valid values:
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grabbles/grabbit | grabbit/core.py | Layout.count | def count(self, entity, files=False):
"""
Return the count of unique values or files for the named entity.
Args:
entity (str): The name of the entity.
files (bool): If True, counts the number of filenames that contain
at least one value of the entity, rat... | python | def count(self, entity, files=False):
"""
Return the count of unique values or files for the named entity.
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entity (str): The name of the entity.
files (bool): If True, counts the number of filenames that contain
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grabbles/grabbit | grabbit/core.py | Layout.as_data_frame | def as_data_frame(self, **kwargs):
"""
Return information for all Files tracked in the Layout as a pandas
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Args:
kwargs: Optional keyword arguments passed on to get(). This allows
one to easily select only a subset of files for export.
Retur... | python | def as_data_frame(self, **kwargs):
"""
Return information for all Files tracked in the Layout as a pandas
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Args:
kwargs: Optional keyword arguments passed on to get(). This allows
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grabbles/grabbit | grabbit/core.py | Layout.build_path | def build_path(self, source, path_patterns=None, strict=False,
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... | python | def build_path(self, source, path_patterns=None, strict=False,
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grabbles/grabbit | grabbit/core.py | Layout.write_contents_to_file | def write_contents_to_file(self, entities, path_patterns=None,
contents=None, link_to=None,
content_mode='text', conflicts='fail',
strict=False, domains=None, index=False,
index_domains=None):
... | python | def write_contents_to_file(self, entities, path_patterns=None,
contents=None, link_to=None,
content_mode='text', conflicts='fail',
strict=False, domains=None, index=False,
index_domains=None):
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flo-compbio/genometools | genometools/misc/log.py | configure_logger | def configure_logger(name, log_stream=sys.stdout, log_file=None,
log_level=logging.INFO, keep_old_handlers=False,
propagate=False):
"""Configures and returns a logger.
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flo-compbio/genometools | genometools/misc/log.py | get_logger | def get_logger(name='', log_stream=None, log_file=None,
quiet=False, verbose=False):
"""Convenience function for getting a logger."""
# configure root logger
log_level = logging.INFO
if quiet:
log_level = logging.WARNING
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log_level = logging.DEBUG
if... | python | def get_logger(name='', log_stream=None, log_file=None,
quiet=False, verbose=False):
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# configure root logger
log_level = logging.INFO
if quiet:
log_level = logging.WARNING
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srevenant/timeinterval | timeinterval/__init__.py | start | def start(milliseconds, func, *args, **kwargs):
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acorg/dark-matter | dark/codonDistance.py | codonInformation | def codonInformation(codons1, codons2):
"""
Take two C{list} of codons, and returns information about the min and
max distance between them.
@param codon1: a C{list} of codons.
@param codon2: a C{list} of codons.
@return: a dict whose keys are C{int} distances and whose values are lists
... | python | def codonInformation(codons1, codons2):
"""
Take two C{list} of codons, and returns information about the min and
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@param codon2: a C{list} of codons.
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vovanec/httputil | examples/http_client.py | example_async_client | def example_async_client(api_client):
"""Example async client.
"""
try:
pprint((yield from api_client.echo()))
except errors.RequestError as exc:
log.exception('Exception occurred: %s', exc)
yield gen.Task(lambda *args, **kwargs: ioloop.IOLoop.current().stop()) | python | def example_async_client(api_client):
"""Example async client.
"""
try:
pprint((yield from api_client.echo()))
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log.exception('Exception occurred: %s', exc)
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vovanec/httputil | examples/http_client.py | example_sync_client | def example_sync_client(api_client):
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vovanec/httputil | examples/http_client.py | main | def main():
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io_loop = ioloop.IOLoop.current()
io_loop.start() | python | def main():
"""Run the examples.
"""
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flo-compbio/genometools | genometools/ensembl/cli/extract_protein_coding_genes.py | main | def main(args=None):
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args: argparse.Namespace object, optional
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shmir/PyIxExplorer | ixexplorer/ixe_statistics_view.py | IxePortsStats.read_stats | def read_stats(self, *stats):
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"""
self.statistics = OrderedDict()
for port in self.ports:
port_stats = IxeStatTotal(port).get_attributes(FLAG_R... | python | def read_stats(self, *stats):
""" Read port statistics from chassis.
:param stats: list of requested statistics to read, if empty - read all statistics.
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shmir/PyIxExplorer | ixexplorer/ixe_statistics_view.py | IxeStreamsStats.read_stats | def read_stats(self, *stats):
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nkavaldj/myhdl_lib | myhdl_lib/arbiter.py | arbiter | def arbiter(rst, clk, req_vec, gnt_vec=None, gnt_idx=None, gnt_vld=None, gnt_rdy=None, ARBITER_TYPE="priority"):
''' Wrapper that provides common interface to all arbiters '''
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''' Wrapper that provides common interface to all arbiters '''
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nkavaldj/myhdl_lib | myhdl_lib/arbiter.py | arbiter_priority | def arbiter_priority(req_vec, gnt_vec=None, gnt_idx=None, gnt_vld=None):
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nkavaldj/myhdl_lib | myhdl_lib/arbiter.py | arbiter_roundrobin | def arbiter_roundrobin(rst, clk, req_vec, gnt_vec=None, gnt_idx=None, gnt_vld=None, gnt_rdy=None):
""" Round Robin arbiter: finds the active request with highest priority and presents its index on the gnt_idx output.
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biocommons/bioutils | src/bioutils/digests.py | seq_seqhash | def seq_seqhash(seq, normalize=True):
"""returns 24-byte Truncated Digest sequence `seq`
>>> seq_seqhash("")
'z4PhNX7vuL3xVChQ1m2AB9Yg5AULVxXc'
>>> seq_seqhash("ACGT")
'aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'
>>> seq_seqhash("acgt")
'aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'
>>> seq_seqhash("acgt"... | python | def seq_seqhash(seq, normalize=True):
"""returns 24-byte Truncated Digest sequence `seq`
>>> seq_seqhash("")
'z4PhNX7vuL3xVChQ1m2AB9Yg5AULVxXc'
>>> seq_seqhash("ACGT")
'aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'
>>> seq_seqhash("acgt")
'aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'
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>>> seq_seqhash("ACGT")
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biocommons/bioutils | src/bioutils/digests.py | seq_seguid | def seq_seguid(seq, normalize=True):
"""returns seguid for sequence `seq`
This seguid is compatible with BioPython's seguid.
>>> seq_seguid('')
'2jmj7l5rSw0yVb/vlWAYkK/YBwk'
>>> seq_seguid('ACGT')
'IQiZThf2zKn/I1KtqStlEdsHYDQ'
>>> seq_seguid('acgt')
'IQiZThf2zKn/I1KtqStlEdsHYDQ'
... | python | def seq_seguid(seq, normalize=True):
"""returns seguid for sequence `seq`
This seguid is compatible with BioPython's seguid.
>>> seq_seguid('')
'2jmj7l5rSw0yVb/vlWAYkK/YBwk'
>>> seq_seguid('ACGT')
'IQiZThf2zKn/I1KtqStlEdsHYDQ'
>>> seq_seguid('acgt')
'IQiZThf2zKn/I1KtqStlEdsHYDQ'
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biocommons/bioutils | src/bioutils/digests.py | seq_md5 | def seq_md5(seq, normalize=True):
"""returns unicode md5 as hex digest for sequence `seq`.
>>> seq_md5('')
'd41d8cd98f00b204e9800998ecf8427e'
>>> seq_md5('ACGT')
'f1f8f4bf413b16ad135722aa4591043e'
>>> seq_md5('ACGT*')
'f1f8f4bf413b16ad135722aa4591043e'
>>> seq_md5(' A C G T ')
'f... | python | def seq_md5(seq, normalize=True):
"""returns unicode md5 as hex digest for sequence `seq`.
>>> seq_md5('')
'd41d8cd98f00b204e9800998ecf8427e'
>>> seq_md5('ACGT')
'f1f8f4bf413b16ad135722aa4591043e'
>>> seq_md5('ACGT*')
'f1f8f4bf413b16ad135722aa4591043e'
>>> seq_md5(' A C G T ')
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biocommons/bioutils | src/bioutils/digests.py | seq_sha1 | def seq_sha1(seq, normalize=True):
"""returns unicode sha1 hexdigest for sequence `seq`.
>>> seq_sha1('')
'da39a3ee5e6b4b0d3255bfef95601890afd80709'
>>> seq_sha1('ACGT')
'2108994e17f6cca9ff2352ada92b6511db076034'
>>> seq_sha1('acgt')
'2108994e17f6cca9ff2352ada92b6511db076034'
>>> seq... | python | def seq_sha1(seq, normalize=True):
"""returns unicode sha1 hexdigest for sequence `seq`.
>>> seq_sha1('')
'da39a3ee5e6b4b0d3255bfef95601890afd80709'
>>> seq_sha1('ACGT')
'2108994e17f6cca9ff2352ada92b6511db076034'
>>> seq_sha1('acgt')
'2108994e17f6cca9ff2352ada92b6511db076034'
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>>> seq_sha1('ACGT')
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biocommons/bioutils | src/bioutils/digests.py | seq_sha512 | def seq_sha512(seq, normalize=True):
"""returns unicode sequence sha512 hexdigest for sequence `seq`.
>>> seq_sha512('')
'cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e'
>>> seq_sha512('ACGT')
'68a178f7c740c5c240aa67... | python | def seq_sha512(seq, normalize=True):
"""returns unicode sequence sha512 hexdigest for sequence `seq`.
>>> seq_sha512('')
'cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e'
>>> seq_sha512('ACGT')
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biocommons/bioutils | src/bioutils/digests.py | seq_vmc_identifier | def seq_vmc_identifier(seq, normalize=True):
"""returns VMC identifier (record) for sequence `seq`
See https://github.com/ga4gh/vmc
>>> seq_vmc_identifier("") == {'namespace': 'VMC', 'accession': 'GS_z4PhNX7vuL3xVChQ1m2AB9Yg5AULVxXc'}
True
>>> seq_vmc_identifier("ACGT") == {'namespace': 'VMC', 'a... | python | def seq_vmc_identifier(seq, normalize=True):
"""returns VMC identifier (record) for sequence `seq`
See https://github.com/ga4gh/vmc
>>> seq_vmc_identifier("") == {'namespace': 'VMC', 'accession': 'GS_z4PhNX7vuL3xVChQ1m2AB9Yg5AULVxXc'}
True
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flo-compbio/genometools | genometools/gcloud/tasks/star.py | map_single_end | def map_single_end(credentials, instance_config, instance_name,
script_dir, index_dir, fastq_file, output_dir,
num_threads=None, seed_start_lmax=None,
mismatch_nmax=None, multimap_nmax=None,
splice_min_overhang=None,
out_mult... | python | def map_single_end(credentials, instance_config, instance_name,
script_dir, index_dir, fastq_file, output_dir,
num_threads=None, seed_start_lmax=None,
mismatch_nmax=None, multimap_nmax=None,
splice_min_overhang=None,
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- recommended machine type: "n1-standard-16" (60 GB of RAM, 16 vCPUs).
- recommended disk size: depends on size of FASTQ files, at least 128 GB.
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flo-compbio/genometools | genometools/gcloud/tasks/star.py | generate_index | def generate_index(credentials, instance_config, instance_name,
script_dir, genome_file, output_dir, annotation_file=None,
splice_overhang=100,
num_threads=8, chromosome_bin_bits=18,
genome_memory_limit=31000000000,
self_dest... | python | def generate_index(credentials, instance_config, instance_name,
script_dir, genome_file, output_dir, annotation_file=None,
splice_overhang=100,
num_threads=8, chromosome_bin_bits=18,
genome_memory_limit=31000000000,
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nkavaldj/myhdl_lib | myhdl_lib/fifo.py | fifo | def fifo(rst, clk, full, we, din, empty, re, dout, afull=None, aempty=None, afull_th=None, aempty_th=None, ovf=None, udf=None, count=None, count_max=None, depth=None, width=None):
""" Synchronous FIFO
Input interface: full, we, din
Output interface: empty, re, dout
It s possible to se... | python | def fifo(rst, clk, full, we, din, empty, re, dout, afull=None, aempty=None, afull_th=None, aempty_th=None, ovf=None, udf=None, count=None, count_max=None, depth=None, width=None):
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Output interface: empty, re, dout
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flo-compbio/genometools | genometools/ensembl/util.py | get_file_checksums | def get_file_checksums(url, ftp=None):
"""Download and parse an Ensembl CHECKSUMS file and obtain checksums.
Parameters
----------
url : str
The URL of the CHECKSUM file.
ftp : `ftplib.FTP` or `None`, optional
An FTP connection.
Returns
-------
`collections.OrderedD... | python | def get_file_checksums(url, ftp=None):
"""Download and parse an Ensembl CHECKSUMS file and obtain checksums.
Parameters
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url : str
The URL of the CHECKSUM file.
ftp : `ftplib.FTP` or `None`, optional
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grabbles/grabbit | grabbit/utils.py | listify | def listify(obj, ignore=(list, tuple, type(None))):
''' Wraps all non-list or tuple objects in a list; provides a simple way
to accept flexible arguments. '''
return obj if isinstance(obj, ignore) else [obj] | python | def listify(obj, ignore=(list, tuple, type(None))):
''' Wraps all non-list or tuple objects in a list; provides a simple way
to accept flexible arguments. '''
return obj if isinstance(obj, ignore) else [obj] | [
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flo-compbio/genometools | genometools/ncbi/taxonomy.py | _get_divisions | def _get_divisions(taxdump_file):
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with tf.extractfile('division.dmp') as fh:
df = pd.read_csv(fh, header=None, sep='|', encoding='ascii')
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vovanec/httputil | httputil/request_engines/sync.py | SyncRequestEngine._request | def _request(self, url, *,
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:rtype: requests.Session
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flo-compbio/genometools | genometools/gdc/tcga.py | get_clinical_data | def get_clinical_data(tcga_id):
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tcga_id : str
The TCGA project ID.
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`pandas.DataFrame`
The clinical data.abs
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tcga_id : str
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flo-compbio/genometools | genometools/gdc/tcga.py | get_biospecimen_data | def get_biospecimen_data(tcga_id):
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tcga_id : str
The TCGA project ID.
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`pandas.DataFrame`
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flo-compbio/genometools | genometools/gdc/tcga.py | get_masked_cnv_manifest | def get_masked_cnv_manifest(tcga_id):
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tcga_id : str
The TCGA project ID.
download_file : str
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... | python | def get_masked_cnv_manifest(tcga_id):
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The TCGA project ID.
download_file : str
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flo-compbio/genometools | genometools/gdc/tcga.py | get_file_samples | def get_file_samples(file_ids):
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flo-compbio/genometools | genometools/gdc/tcga.py | get_unique_sample_files | def get_unique_sample_files(file_samples):
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A data frame containing a mapping between file IDs and sample barcodes.
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Params
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A data frame containing a mapping between file IDs and sample barcodes.
This type of data frame is returned by :meth:`get_file_samples`.
Returns
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flo-compbio/genometools | genometools/gdc/tcga.py | get_fresh_primary_tumors | def get_fresh_primary_tumors(biospecimen):
"""Filter biospecimen data to only keep non-FFPE primary tumor samples.
Parameters
----------
biospecimen : `pandas.DataFrame`
The biospecimen data frame. This type of data frame is returned by
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Returns... | python | def get_fresh_primary_tumors(biospecimen):
"""Filter biospecimen data to only keep non-FFPE primary tumor samples.
Parameters
----------
biospecimen : `pandas.DataFrame`
The biospecimen data frame. This type of data frame is returned by
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acorg/dark-matter | dark/fasta.py | dedupFasta | def dedupFasta(reads):
"""
Remove sequence duplicates (based on sequence) from FASTA.
@param reads: a C{dark.reads.Reads} instance.
@return: a generator of C{dark.reads.Read} instances with no duplicates.
"""
seen = set()
add = seen.add
for read in reads:
hash_ = md5(read.sequen... | python | def dedupFasta(reads):
"""
Remove sequence duplicates (based on sequence) from FASTA.
@param reads: a C{dark.reads.Reads} instance.
@return: a generator of C{dark.reads.Read} instances with no duplicates.
"""
seen = set()
add = seen.add
for read in reads:
hash_ = md5(read.sequen... | [
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acorg/dark-matter | dark/fasta.py | dePrefixAndSuffixFasta | def dePrefixAndSuffixFasta(sequences):
"""
sequences: an iterator producing Bio.Seq sequences.
return: a generator of sequences with no duplicates and no fully contained
subsequences.
"""
sequences = sorted(sequences, key=lambda s: len(s.seq), reverse=True)
seen = set()
for s in seq... | python | def dePrefixAndSuffixFasta(sequences):
"""
sequences: an iterator producing Bio.Seq sequences.
return: a generator of sequences with no duplicates and no fully contained
subsequences.
"""
sequences = sorted(sequences, key=lambda s: len(s.seq), reverse=True)
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acorg/dark-matter | dark/fasta.py | fastaSubtract | def fastaSubtract(fastaFiles):
"""
Given a list of open file descriptors, each with FASTA content,
remove the reads found in the 2nd, 3rd, etc files from the first file
in the list.
@param fastaFiles: a C{list} of FASTA filenames.
@raises IndexError: if passed an empty list.
@return: An ite... | python | def fastaSubtract(fastaFiles):
"""
Given a list of open file descriptors, each with FASTA content,
remove the reads found in the 2nd, 3rd, etc files from the first file
in the list.
@param fastaFiles: a C{list} of FASTA filenames.
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acorg/dark-matter | dark/fasta.py | combineReads | def combineReads(filename, sequences, readClass=DNARead,
upperCase=False, idPrefix='command-line-read-'):
"""
Combine FASTA reads from a file and/or sequence strings.
@param filename: A C{str} file name containing FASTA reads.
@param sequences: A C{list} of C{str} sequences. If a seque... | python | def combineReads(filename, sequences, readClass=DNARead,
upperCase=False, idPrefix='command-line-read-'):
"""
Combine FASTA reads from a file and/or sequence strings.
@param filename: A C{str} file name containing FASTA reads.
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acorg/dark-matter | dark/fasta.py | FastaReads.iter | def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
as an instance of the desired read class.
"""
count = 0
for _file in self._files:
with asHandle(_file) as fp:
# Duplicate some code here so as not to test... | python | def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
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count = 0
for _file in self._files:
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acorg/dark-matter | dark/fasta.py | FastaFaiReads.iter | def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
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"""
if self._upperCase:
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... | python | def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
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"""
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for id_ in self._fasta:
yield self._readClass(id_, str(self._fasta[id_]).upper())
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acorg/dark-matter | dark/fasta.py | SqliteIndex._getFilename | def _getFilename(self, fileNumber):
"""
Given a file number, get its name (if any).
@param fileNumber: An C{int} file number.
@return: A C{str} file name or C{None} if a file with that number
has not been added.
"""
cur = self._connection.cursor()
cur... | python | def _getFilename(self, fileNumber):
"""
Given a file number, get its name (if any).
@param fileNumber: An C{int} file number.
@return: A C{str} file name or C{None} if a file with that number
has not been added.
"""
cur = self._connection.cursor()
cur... | [
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acorg/dark-matter | dark/fasta.py | SqliteIndex._getFileNumber | def _getFileNumber(self, filename):
"""
Given a file name, get its file number (if any).
@param filename: A C{str} file name.
@return: An C{int} file number or C{None} if no file with that name
has been added.
"""
cur = self._connection.cursor()
cur.e... | python | def _getFileNumber(self, filename):
"""
Given a file name, get its file number (if any).
@param filename: A C{str} file name.
@return: An C{int} file number or C{None} if no file with that name
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"""
cur = self._connection.cursor()
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acorg/dark-matter | dark/fasta.py | SqliteIndex._addFilename | def _addFilename(self, filename):
"""
Add a new file name.
@param filename: A C{str} file name.
@raise ValueError: If a file with this name has already been added.
@return: The C{int} id of the newly added file.
"""
cur = self._connection.cursor()
try:
... | python | def _addFilename(self, filename):
"""
Add a new file name.
@param filename: A C{str} file name.
@raise ValueError: If a file with this name has already been added.
@return: The C{int} id of the newly added file.
"""
cur = self._connection.cursor()
try:
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acorg/dark-matter | dark/fasta.py | SqliteIndex.addFile | def addFile(self, filename):
"""
Add a new FASTA file of sequences.
@param filename: A C{str} file name, with the file in FASTA format.
This file must (obviously) exist at indexing time. When __getitem__
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... | python | def addFile(self, filename):
"""
Add a new FASTA file of sequences.
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acorg/dark-matter | dark/fasta.py | SqliteIndex._find | def _find(self, id_):
"""
Find the filename and offset of a sequence, given its id.
@param id_: A C{str} sequence id.
@return: A 2-tuple, containing the C{str} file name and C{int} offset
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"""
cur = self._connection.cursor()
... | python | def _find(self, id_):
"""
Find the filename and offset of a sequence, given its id.
@param id_: A C{str} sequence id.
@return: A 2-tuple, containing the C{str} file name and C{int} offset
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flo-compbio/genometools | genometools/gtf.py | parse_attributes | def parse_attributes(s):
""" Parses the ``attribute`` string of a GFF/GTF annotation.
Parameters
----------
s : str
The attribute string.
Returns
-------
dict
A dictionary containing attribute name/value pairs.
Notes
-----
The ``attribute`` string is the 9th fi... | python | def parse_attributes(s):
""" Parses the ``attribute`` string of a GFF/GTF annotation.
Parameters
----------
s : str
The attribute string.
Returns
-------
dict
A dictionary containing attribute name/value pairs.
Notes
-----
The ``attribute`` string is the 9th fi... | [
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A dictionary containing attribute name/value pairs.
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