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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData._parse_segments | def _parse_segments(self):
""" Read the segment output file and parse into an SQLite database.
"""
reader = csv.reader(open(self._segment_file, 'rU'),
delimiter='\t')
for row in reader:
if reader.line_num == 1: # skip header
contin... | python | def _parse_segments(self):
""" Read the segment output file and parse into an SQLite database.
"""
reader = csv.reader(open(self._segment_file, 'rU'),
delimiter='\t')
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if reader.line_num == 1: # skip header
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.get_multiplicon_leaves | def get_multiplicon_leaves(self, redundant=False):
""" Return a generator of the IDs of multiplicons found at leaves
of the tree (i.e. from which no further multiplicons were derived).
Arguments:
o redundant - if true, report redundant multiplicons
"""
for n... | python | def get_multiplicon_leaves(self, redundant=False):
""" Return a generator of the IDs of multiplicons found at leaves
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.get_multiplicon_seeds | def get_multiplicon_seeds(self, redundant=False):
""" Return a generator of the IDs of multiplicons that are initial
seeding 'pairs' in level 2 multiplicons.
Arguments:
o redundant - if true, report redundant multiplicons
"""
for node in self._multiplicon_gr... | python | def get_multiplicon_seeds(self, redundant=False):
""" Return a generator of the IDs of multiplicons that are initial
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.get_multiplicon_intermediates | def get_multiplicon_intermediates(self, redundant=False):
""" Return a generator of the IDs of multiplicons that are neither
seeding 'pairs' in level 2 multiplicons, nor leaves.
Arguments:
o redundant - if true, report redundant multiplicons
"""
for node in ... | python | def get_multiplicon_intermediates(self, redundant=False):
""" Return a generator of the IDs of multiplicons that are neither
seeding 'pairs' in level 2 multiplicons, nor leaves.
Arguments:
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.get_multiplicon_properties | def get_multiplicon_properties(self, value):
""" Return a dictionary describing multiplicon data:
id, parent, level, number_of_anchorpoints, profile_length,
is_redundant and the contributing genome segments
"""
sql = '''SELECT id, parent, level, number_of_anchorpoints,
... | python | def get_multiplicon_properties(self, value):
""" Return a dictionary describing multiplicon data:
id, parent, level, number_of_anchorpoints, profile_length,
is_redundant and the contributing genome segments
"""
sql = '''SELECT id, parent, level, number_of_anchorpoints,
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.get_multiplicon_segments | def get_multiplicon_segments(self, value):
""" Return a dictionary describing the genome segments that
contribute to the named multiplicon, keyed by genome, with
(start feature, end feature) tuples.
"""
sql = '''SELECT genome, first, last FROM segments
... | python | def get_multiplicon_segments(self, value):
""" Return a dictionary describing the genome segments that
contribute to the named multiplicon, keyed by genome, with
(start feature, end feature) tuples.
"""
sql = '''SELECT genome, first, last FROM segments
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.get_multiplicons_at_level | def get_multiplicons_at_level(self, level, redundant=False):
""" Return a list of IDs of multiplicons at the requested level
"""
sql = '''SELECT id FROM multiplicons
WHERE level=:level'''
cur = self._dbconn.cursor()
cur.execute(sql, {'level': str(level)})
... | python | def get_multiplicons_at_level(self, level, redundant=False):
""" Return a list of IDs of multiplicons at the requested level
"""
sql = '''SELECT id FROM multiplicons
WHERE level=:level'''
cur = self._dbconn.cursor()
cur.execute(sql, {'level': str(level)})
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.is_redundant_multiplicon | def is_redundant_multiplicon(self, value):
""" Returns True if the passed multiplicon ID is redundant, False
otherwise.
- value, (int) multiplicon ID
"""
if not hasattr(self, '_redundant_multiplicon_cache'):
sql = '''SELECT id FROM multiplicons WHERE is_redun... | python | def is_redundant_multiplicon(self, value):
""" Returns True if the passed multiplicon ID is redundant, False
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- value, (int) multiplicon ID
"""
if not hasattr(self, '_redundant_multiplicon_cache'):
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.write | def write(self, mfile="multiplicons.txt", sfile="segments.txt",
clobber=False):
""" Writes multiplicon and segment files to the named locations.
- mfile, (str) location for multiplicons file
- sfile, (str) location for segments file
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData._write_multiplicons | def _write_multiplicons(self, filename):
""" Write multiplicons to file.
- filename, (str) location of output file
"""
# Column headers
mhead = '\t'.join(['id', 'genome_x', 'list_x', 'parent', 'genome_y',
'list_y', 'level', 'number_of_anchorpoints'... | python | def _write_multiplicons(self, filename):
""" Write multiplicons to file.
- filename, (str) location of output file
"""
# Column headers
mhead = '\t'.join(['id', 'genome_x', 'list_x', 'parent', 'genome_y',
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData._write_segments | def _write_segments(self, filename):
""" Write segments to file.
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.multiplicon_file | def multiplicon_file(self, value):
""" Setter for _multiplicon_file attribute """
assert os.path.isfile(value), "%s is not a valid file" % value
self._multiplicon_file = value | python | def multiplicon_file(self, value):
""" Setter for _multiplicon_file attribute """
assert os.path.isfile(value), "%s is not a valid file" % value
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.segment_file | def segment_file(self, value):
""" Setter for _segment_file attribute """
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self._segment_file = value | python | def segment_file(self, value):
""" Setter for _segment_file attribute """
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""" Setter for _db_file attribute """
assert not os.path.isfile(value), "%s already exists" % value
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widdowquinn/pyADHoRe | pyadhore/iadhore.py | IadhoreData.multiplicons | def multiplicons(self):
""" Multiplicon table from SQLite database. """
sql = '''SELECT * FROM multiplicons'''
cur = self._dbconn.cursor()
cur.execute(sql)
data = [r for r in cur.fetchall()]
cur.close()
return data | python | def multiplicons(self):
""" Multiplicon table from SQLite database. """
sql = '''SELECT * FROM multiplicons'''
cur = self._dbconn.cursor()
cur.execute(sql)
data = [r for r in cur.fetchall()]
cur.close()
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lemieuxl/pyGenClean | pyGenClean/PlinkUtils/compare_bim.py | main | def main():
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lemieuxl/pyGenClean | pyGenClean/PlinkUtils/compare_bim.py | compareSNPs | def compareSNPs(before, after, outFileName):
"""Compares two set of SNPs.
:param before: the names of the markers in the ``before`` file.
:param after: the names of the markers in the ``after`` file.
:param outFileName: the name of the output file.
:type before: set
:type after: set
:type ... | python | def compareSNPs(before, after, outFileName):
"""Compares two set of SNPs.
:param before: the names of the markers in the ``before`` file.
:param after: the names of the markers in the ``after`` file.
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lemieuxl/pyGenClean | pyGenClean/PlinkUtils/compare_bim.py | readBIM | def readBIM(fileName):
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lemieuxl/pyGenClean | pyGenClean/PlinkUtils/compare_bim.py | checkArgs | def checkArgs(args):
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:returns: ``True`` if everything was OK.
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emdb-empiar/ahds | ahds/header.py | Block.add_attr | def add_attr(self, name, value):
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emdb-empiar/ahds | ahds/header.py | AmiraHeader.from_file | def from_file(cls, fn, *args, **kwargs):
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:return ah: object of class ``AmiraHeader`` containing header metadata
:rtype: ah: :py:class:`ahds.header.AmiraHeader`
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return AmiraHea... | python | def from_file(cls, fn, *args, **kwargs):
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wolfhong/formic | formic/formic.py | get_version | def get_version():
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# Try with the package manager, if present
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wolfhong/formic | formic/formic.py | get_path_components | def get_path_components(directory):
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previou... | python | def get_path_components(directory):
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wolfhong/formic | formic/formic.py | reconstitute_path | def reconstitute_path(drive, folders):
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:param folders: A list of folder names
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wolfhong/formic | formic/formic.py | Matcher.create | def create(pattern, casesensitive=True):
"""Factory for :class:`Matcher` instances; returns a :class:`Matcher`
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casesensitive = determine_casesensitive(casesensitive)
if "?" in pattern or "*" in pattern:
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"""Factory for :class:`Matcher` instances; returns a :class:`Matcher`
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wolfhong/formic | formic/formic.py | FNMatcher.match | def match(self, string):
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wolfhong/formic | formic/formic.py | Section.match_iter | def match_iter(self, path_elements, start_at):
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wolfhong/formic | formic/formic.py | Section._match_iter_generic | def _match_iter_generic(self, path_elements, start_at):
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wolfhong/formic | formic/formic.py | Section._match_iter_single | def _match_iter_single(self, path_elements, start_at):
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wolfhong/formic | formic/formic.py | Pattern._simplify | def _simplify(elements):
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wolfhong/formic | formic/formic.py | Pattern.match_directory | def match_directory(self, path_elements):
"""Returns a :class:`MatchType` for the directory, expressed as a list of path
elements, match for the :class:`Pattern`.
If ``self.bound_start`` is True, the first :class:`Section` must match
from the first directory element.
If ``self.... | python | def match_directory(self, path_elements):
"""Returns a :class:`MatchType` for the directory, expressed as a list of path
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wolfhong/formic | formic/formic.py | Pattern.match_files | def match_files(self, matched, unmatched):
"""Moves all matching files from the set *unmatched* to the set
*matched*.
Both *matched* and *unmatched* are sets of string, the strings
being unqualified file names"""
this_match = set(self.file_filter(unmatched))
matched |= t... | python | def match_files(self, matched, unmatched):
"""Moves all matching files from the set *unmatched* to the set
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Both *matched* and *unmatched* are sets of string, the strings
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wolfhong/formic | formic/formic.py | Pattern._to_string | def _to_string(self):
"""Implemented a function for __str__ and __repr__ to use, but
which prevents infinite recursion when migrating to Python 3"""
if self.sections:
start = "/" if self.bound_start else "**/"
sections = "/**/".join(str(section) for section in self.sectio... | python | def _to_string(self):
"""Implemented a function for __str__ and __repr__ to use, but
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start = "/" if self.bound_start else "**/"
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wolfhong/formic | formic/formic.py | PatternSet._compute_all_files | def _compute_all_files(self):
"""Handles lazy evaluation of self.all_files"""
self._all_files = any(pat.all_files() for pat in self.patterns) | python | def _compute_all_files(self):
"""Handles lazy evaluation of self.all_files"""
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wolfhong/formic | formic/formic.py | PatternSet.append | def append(self, pattern):
"""Adds a :class:`Pattern` to the :class:`PatternSet`"""
assert isinstance(pattern, Pattern)
self.patterns.append(pattern)
if self._all_files is not None:
self._all_files = self._all_files or pattern.all_files() | python | def append(self, pattern):
"""Adds a :class:`Pattern` to the :class:`PatternSet`"""
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wolfhong/formic | formic/formic.py | PatternSet.extend | def extend(self, patterns):
"""Extend a :class:`PatternSet` with addition *patterns*
*patterns* can either be:
* A single :class:`Pattern`
* Another :class:`PatternSet` or
* A list of :class:`Pattern` instances"""
assert patterns is not None
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wolfhong/formic | formic/formic.py | PatternSet.remove | def remove(self, pattern):
"""Remove a :class:`Pattern` from the :class:`PatternSet`"""
assert isinstance(pattern, Pattern)
self.patterns.remove(pattern)
self._all_files = None | python | def remove(self, pattern):
"""Remove a :class:`Pattern` from the :class:`PatternSet`"""
assert isinstance(pattern, Pattern)
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wolfhong/formic | formic/formic.py | PatternSet.match_files | def match_files(self, matched, unmatched):
"""Apply the include and exclude filters to those files in *unmatched*,
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set.
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wolfhong/formic | formic/formic.py | PatternSet.iter | def iter(self):
"""An iteration generator that allows the loop to modify the
:class:`PatternSet` during the loop"""
if self.patterns:
patterns = list(self.patterns)
for pattern in patterns:
yield pattern | python | def iter(self):
"""An iteration generator that allows the loop to modify the
:class:`PatternSet` during the loop"""
if self.patterns:
patterns = list(self.patterns)
for pattern in patterns:
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wolfhong/formic | formic/formic.py | FileSetState._find_parent | def _find_parent(self, path_elements):
"""Recurse up the tree of FileSetStates until we find a parent, i.e.
one whose path_elements member is the start of the path_element
argument"""
if not self.path_elements:
# Automatically terminate on root
return self
... | python | def _find_parent(self, path_elements):
"""Recurse up the tree of FileSetStates until we find a parent, i.e.
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wolfhong/formic | formic/formic.py | FileSetState._matching_pattern_sets | def _matching_pattern_sets(self):
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"""Returns an iterator containing all PatternSets that match this
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wolfhong/formic | formic/formic.py | FileSetState.match | def match(self, files):
"""Given a set of files in this directory, returns all the files that
match the :class:`Pattern` instances which match this directory."""
if not files:
return set()
if (self.matched_inherit.all_files()
or self.matched_and_subdir.all_fi... | python | def match(self, files):
"""Given a set of files in this directory, returns all the files that
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wolfhong/formic | formic/formic.py | FileSetState.no_possible_matches_in_subdirs | def no_possible_matches_in_subdirs(self):
"""Returns True if there are no possible matches for any
subdirectories of this :class:`FileSetState`.
When this :class:FileSetState is used for an 'include', a return of
`True` means we can exclude all subdirectories."""
return (not sel... | python | def no_possible_matches_in_subdirs(self):
"""Returns True if there are no possible matches for any
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When this :class:FileSetState is used for an 'include', a return of
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wolfhong/formic | formic/formic.py | FileSet._preprocess | def _preprocess(argument, casesensitive):
"""Receives the argument (from the constructor), and normalizes it
into a list of Pattern objects."""
pattern_set = PatternSet()
if argument is not None:
if isinstance(argument, STRING_TYPES):
argument = [argument, ]
... | python | def _preprocess(argument, casesensitive):
"""Receives the argument (from the constructor), and normalizes it
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pattern_set = PatternSet()
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wolfhong/formic | formic/formic.py | FileSet.get_directory | def get_directory(self):
"""Returns the directory in which the :class:`FileSet` will be run.
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"""Returns the directory in which the :class:`FileSet` will be run.
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wolfhong/formic | formic/formic.py | FileSet._receive | def _receive(self, root, directory, dirs, files, include, exclude):
"""Internal function processing each yield from os.walk."""
self._received += 1
if not self.symlinks:
where = root + os.path.sep + directory + os.path.sep
files = [
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The generator yields a tuple of ``(rel_dir_name, file_name)``:
1. *rel_dir_name*: The path relative to the starting directory
2. *file_name*: The unqualified file name
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | main | def main(argString=None):
"""The main function of this module.
:param argString: the options.
:type argString: list of strings
"""
# Getting and checking the options
args = parseArgs(argString)
checkArgs(args)
logger.info("Options used:")
for key, value in vars(args).iteritems():... | python | def main(argString=None):
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:type argString: list of strings
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | order_qc_dir | def order_qc_dir(dirnames):
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:param dirnames: the list of directories to merge data from.
:type dirnames: list
:returns: the sorted list of directories
:rtype: list
"""
return sorted(
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | merge_required_files | def merge_required_files(dirnames, out_dir):
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:param out_dir: the name of the output directory.
:type dirnames: list
:type out_dir: str
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:type dirnames: list
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | get_final_numbers | def get_final_numbers(filename, out_dir):
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:param out_dir: the output directory.
:type filename: str
:type out_dir: str
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | get_summary_files | def get_summary_files(dirnames):
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:param dirnames: the list of directories to merge data from.
:type dirnames: list
:returns: a list of summary file names.
:rtype: list
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | generate_report | def generate_report(out_dir, latex_summaries, nb_markers, nb_samples, options):
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:param out_dir: the output directory.
:param latex_summaries: the list of LaTeX summaries.
:param nb_markers: the final number of markers.
:param nb_samples: the final number of samples.
:pa... | python | def generate_report(out_dir, latex_summaries, nb_markers, nb_samples, options):
"""Generates the report.
:param out_dir: the output directory.
:param latex_summaries: the list of LaTeX summaries.
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | checkArgs | def checkArgs(args):
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:type args: argparse.Namespace
:returns: ``True`` if everything was OK.
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:param args: an object containing the options of the program.
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lemieuxl/pyGenClean | pyGenClean/LaTeX/merge_reports.py | add_custom_options | def add_custom_options(parser):
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:param parser: the parser to which to add options.
:type parser: argparse.ArgumentParser
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... | python | def add_custom_options(parser):
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:param parser: the parser to which to add options.
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | main | def main(argString=None):
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | plot_related_data | def plot_related_data(x, y, code, ylabel, fileName, options):
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:param x: the x axis of the plot (``IBS2 ratio``).
:param y: the y axis of the plot (either ``z1`` or ``z2``).
:param code: the code of the relatedness of each sample pair.
:param ylabel: the... | python | def plot_related_data(x, y, code, ylabel, fileName, options):
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:param x: the x axis of the plot (``IBS2 ratio``).
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | extractRelatedIndividuals | def extractRelatedIndividuals(fileName, outPrefix, ibs2_ratio_threshold):
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:param fileName: the name of the input file.
:param outPrefix: the prefix of the output files.
:param ibs2_ratio_threshold: the ibs2 ratio threshold (tells if sample pair
... | python | def extractRelatedIndividuals(fileName, outPrefix, ibs2_ratio_threshold):
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | checkNumberOfSNP | def checkNumberOfSNP(fileName, minimumNumber):
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:param fileName: the name of the file.
:param minimumNumber: the minimum number of markers that needs to be in the
file.
:type fileName: str
:type minimumNumber: int
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | splitFile | def splitFile(inputFileName, linePerFile, outPrefix):
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:param linePerFile: the number of line per file (after splitting).
:param outPrefix: the prefix of the output files.
:type inputFileName: str
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:typ... | python | def splitFile(inputFileName, linePerFile, outPrefix):
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:param inputFileName: the name of the input file.
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | runGenome | def runGenome(bfile, options):
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:param bfile: the input file prefix.
:param options: the options.
:type bfile: str
:type options: argparse.Namespace
:returns: the name of the ``genome`` file.
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:param bfile: the input file prefix.
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | mergeGenomeLogFiles | def mergeGenomeLogFiles(outPrefix, nbSet):
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | runGenomeSGE | def runGenomeSGE(bfile, freqFile, nbJob, outPrefix, options):
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | extractSNPs | def extractSNPs(snpsToExtract, options):
"""Extract markers using Plink.
:param snpsToExtract: the name of the file containing markers to extract.
:param options: the options
:type snpsToExtract: str
:type options: argparse.Namespace
:returns: the prefix of the output files.
"""
outP... | python | def extractSNPs(snpsToExtract, options):
"""Extract markers using Plink.
:param snpsToExtract: the name of the file containing markers to extract.
:param options: the options
:type snpsToExtract: str
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | selectSNPsAccordingToLD | def selectSNPsAccordingToLD(options):
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:type options: argparse.Namespace
:returns: the name of the output file (from Plink).
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# The plink command
outPrefix = options.out + ".pruning_" + options.indep_pairwise[2]
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lemieuxl/pyGenClean | pyGenClean/RelatedSamples/find_related_samples.py | checkArgs | def checkArgs(args):
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:type args: argparse.Namespace
:returns: ``True`` if everything was OK.
If there is a problem with an option, an exception is raised using the
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"""Checks the arguments and options.
:param args: an object containing the options of the program.
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OTL/jps | jps/subscriber.py | Subscriber.spin_once | def spin_once(self, polling_sec=0.010):
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>>> def callback(msg):
... print msg
>>> sub = jps.Subscriber('topic_name', callback)
>>> try:
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>>> def callback(msg):
... print msg
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'''receive next data (block until next data)'''
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vinitkumar/pycrawler | linkfetcher.py | Linkfetcher.open | def open(self):
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url = self.url
try:
request = urllib.request.Request(url)
handle = urllib.request.build_opener()
except IOError:
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return (request, handle) | python | def open(self):
"""Open the URL with urllib.request."""
url = self.url
try:
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except IOError:
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vinitkumar/pycrawler | linkfetcher.py | Linkfetcher._get_crawled_urls | def _get_crawled_urls(self, handle, request):
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photo/openphoto-python | trovebox/objects/album.py | Album._update_fields_with_objects | def _update_fields_with_objects(self):
""" Convert dict fields into objects, where appropriate """
# Update the cover with a photo object
if isinstance(self.cover, dict):
self.cover = Photo(self._client, self.cover)
# Update the photo list with photo objects
try:
... | python | def _update_fields_with_objects(self):
""" Convert dict fields into objects, where appropriate """
# Update the cover with a photo object
if isinstance(self.cover, dict):
self.cover = Photo(self._client, self.cover)
# Update the photo list with photo objects
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photo/openphoto-python | trovebox/objects/album.py | Album.cover_update | def cover_update(self, photo, **kwds):
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Endpoint: /album/<album_id>/cover/<photo_id>/update.json
Update the cover photo of this album.
"""
result = self._client.album.cover_update(self, photo, **kwds)
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"""
Endpoint: /album/<album_id>/cover/<photo_id>/update.json
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result = self._client.album.cover_update(self, photo, **kwds)
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photo/openphoto-python | trovebox/objects/album.py | Album.delete | def delete(self, **kwds):
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Endpoint: /album/<id>/delete.json
Deletes this album.
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Raises a TroveboxError if not.
"""
result = self._client.album.delete(self, **kwds)
self._delete_fields()
return result | python | def delete(self, **kwds):
"""
Endpoint: /album/<id>/delete.json
Deletes this album.
Returns True if successful.
Raises a TroveboxError if not.
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result = self._client.album.delete(self, **kwds)
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photo/openphoto-python | trovebox/objects/album.py | Album.add | def add(self, objects, object_type=None, **kwds):
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Endpoint: /album/<id>/<type>/add.json
Add objects (eg. Photos) to this album.
The objects are a list of either IDs or Trovebox objects.
If Trovebox objects are used, the object type is inferred
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"""
Endpoint: /album/<id>/<type>/add.json
Add objects (eg. Photos) to this album.
The objects are a list of either IDs or Trovebox objects.
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"""
Decorate the handle method with a file lock to ensure there is only ever
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"""
def wrapper(self, *args, **options):
def on_interrupt(signum, frame):
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sys.exit()
... | python | def handle_lock(handle):
"""
Decorate the handle method with a file lock to ensure there is only ever
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"""
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emdb-empiar/ahds | ahds/data_stream.py | hxbyterle_decode | def hxbyterle_decode(output_size, data):
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emdb-empiar/ahds | ahds/data_stream.py | hxzip_decode | def hxzip_decode(data_size, data):
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:param str data: a raw stream of data to be unpacked
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"""Decode HxZip data stream
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emdb-empiar/ahds | ahds/data_stream.py | unpack_binary | def unpack_binary(data_pointer, definitions, data):
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emdb-empiar/ahds | ahds/data_stream.py | unpack_ascii | def unpack_ascii(data):
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emdb-empiar/ahds | ahds/data_stream.py | Image.as_contours | def as_contours(self):
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emdb-empiar/ahds | ahds/data_stream.py | Image.show | def show(self):
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emdb-empiar/ahds | ahds/data_stream.py | AmiraMeshDataStream.to_volume | def to_volume(self):
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sveetch/django-icomoon | icomoon/store.py | WebfontStore.parse_manifest | def parse_manifest(self, fp):
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Open manifest JSON file and build icon map
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sveetch/django-icomoon | icomoon/store.py | WebfontStore.get | def get(self, webfont_name, webfont_settings):
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sveetch/django-icomoon | icomoon/store.py | WebfontStore.fetch | def fetch(self, webfonts):
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webfonts (dict): Dictionnary of webfont settings from
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winkidney/cmdtree | src/cmdtree/shortcuts.py | _apply2parser | def _apply2parser(arguments, options, parser):
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winkidney/cmdtree | src/cmdtree/shortcuts.py | apply2parser | def apply2parser(cmd_proxy, parser):
"""
Apply a CmdProxy's arguments and options
to a parser of argparse.
:type cmd_proxy: callable or CmdProxy
:type parser: cmdtree.parser.AParser
:rtype: cmdtree.parser.AParser
"""
if isinstance(cmd_proxy, CmdProxy):
parser_proxy = cmd_proxy.me... | python | def apply2parser(cmd_proxy, parser):
"""
Apply a CmdProxy's arguments and options
to a parser of argparse.
:type cmd_proxy: callable or CmdProxy
:type parser: cmdtree.parser.AParser
:rtype: cmdtree.parser.AParser
"""
if isinstance(cmd_proxy, CmdProxy):
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radujica/baloo | baloo/io/csv.py | read_csv | def read_csv(filepath, sep=',', header='infer', names=None, usecols=None, dtype=None, converters=None,
skiprows=None, nrows=None):
"""Read CSV into DataFrame.
Eager implementation using pandas, i.e. entire file is read at this point. Only common/relevant parameters
available at the moment; for... | python | def read_csv(filepath, sep=',', header='infer', names=None, usecols=None, dtype=None, converters=None,
skiprows=None, nrows=None):
"""Read CSV into DataFrame.
Eager implementation using pandas, i.e. entire file is read at this point. Only common/relevant parameters
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radujica/baloo | baloo/io/csv.py | to_csv | def to_csv(df, filepath, sep=',', header=True, index=True):
"""Save DataFrame as csv.
Note data is expected to be evaluated.
Currently delegates to Pandas.
Parameters
----------
df : DataFrame
filepath : str
sep : str, optional
Separator used between values.
header : bool,... | python | def to_csv(df, filepath, sep=',', header=True, index=True):
"""Save DataFrame as csv.
Note data is expected to be evaluated.
Currently delegates to Pandas.
Parameters
----------
df : DataFrame
filepath : str
sep : str, optional
Separator used between values.
header : bool,... | [
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bede/tictax | tictax/cli.py | kmer_lca | def kmer_lca(seqs_path: 'path to (optionally gzipped) fasta/fastq input',
fastq: 'input is fastq; disable autodetection' = False,
progress: 'show progress bar (sent to stderr)' = False):
'''
Lowest common ancestor sequence assignment using the One Codex API.
Streams annotated recor... | python | def kmer_lca(seqs_path: 'path to (optionally gzipped) fasta/fastq input',
fastq: 'input is fastq; disable autodetection' = False,
progress: 'show progress bar (sent to stderr)' = False):
'''
Lowest common ancestor sequence assignment using the One Codex API.
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Streams annotated records to stdout in fasta format.
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bede/tictax | tictax/cli.py | annotate_diamond | def annotate_diamond(fasta_path: 'path to fasta input',
diamond_path: 'path to Diamond taxonomic classification output'):
'''
Annotate fasta headers with taxonomy information from Diamond
'''
records = tictax.parse_seqs(fasta_path)
annotated_records = tictax.annotate_diamond(rec... | python | def annotate_diamond(fasta_path: 'path to fasta input',
diamond_path: 'path to Diamond taxonomic classification output'):
'''
Annotate fasta headers with taxonomy information from Diamond
'''
records = tictax.parse_seqs(fasta_path)
annotated_records = tictax.annotate_diamond(rec... | [
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bede/tictax | tictax/cli.py | filter_taxa | def filter_taxa(fasta_path: 'path to fasta input',
taxids: 'comma delimited list of taxon IDs',
unclassified: 'pass sequences unclassified at superkingdom level >(0)' = False,
discard: 'discard specified taxa' = False,
warnings: 'show warnings' = False):
... | python | def filter_taxa(fasta_path: 'path to fasta input',
taxids: 'comma delimited list of taxon IDs',
unclassified: 'pass sequences unclassified at superkingdom level >(0)' = False,
discard: 'discard specified taxa' = False,
warnings: 'show warnings' = False):
... | [
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bede/tictax | tictax/cli.py | matrix | def matrix(fasta_path: 'path to tictax annotated fasta input',
scafstats_path: 'path to BBMap scaftstats file'):
'''
Generate taxonomic count matrix from tictax classified contigs
'''
records = SeqIO.parse(fasta_path, 'fasta')
df = tictax.matrix(records, scafstats_path)
df.to_csv(sys.... | python | def matrix(fasta_path: 'path to tictax annotated fasta input',
scafstats_path: 'path to BBMap scaftstats file'):
'''
Generate taxonomic count matrix from tictax classified contigs
'''
records = SeqIO.parse(fasta_path, 'fasta')
df = tictax.matrix(records, scafstats_path)
df.to_csv(sys.... | [
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