_id
stringlengths 2
7
| title
stringlengths 1
88
| partition
stringclasses 3
values | text
stringlengths 31
13.1k
| language
stringclasses 1
value | meta_information
dict |
|---|---|---|---|---|---|
q2100
|
TwitterStream.datagramReceived
|
train
|
def datagramReceived(self, data):
"""
Decode the JSON-encoded datagram and call the callback.
"""
try:
obj = json.loads(data)
except ValueError, e:
log.err(e, 'Invalid JSON in stream: %r' % data)
return
|
python
|
{
"resource": ""
}
|
q2101
|
TwitterStream.connectionLost
|
train
|
def connectionLost(self, reason):
"""
Called when the body is complete or the connection was lost.
@note: As the body length is usually not known at the beginning of the
response we expect a L{PotentialDataLoss} when Twitter closes the
stream, instead of L{ResponseDone}. Other exceptions are treated
as error conditions.
|
python
|
{
"resource": ""
}
|
q2102
|
simpleListFactory
|
train
|
def simpleListFactory(list_type):
"""Used for simple parsers that support only one type of object"""
def create(delegate, extra_args=None):
"""Create a Parser object for the specific tag type,
|
python
|
{
"resource": ""
}
|
q2103
|
BaseXMLHandler.setSubDelegates
|
train
|
def setSubDelegates(self, namelist, before=None, after=None):
"""Set a delegate for a sub-sub-item, according to a list of names"""
if len(namelist) > 1:
def set_sub(i):
i.setSubDelegates(namelist[1:], before, after)
|
python
|
{
"resource": ""
}
|
q2104
|
_split_path
|
train
|
def _split_path(path):
"""split a path return by the api
return
- the sentinel:
- the rest of the path as a list.
- the original path stripped of / for normalisation.
|
python
|
{
"resource": ""
}
|
q2105
|
MixedContentsManager.path_dispatch_rename
|
train
|
def path_dispatch_rename(rename_like_method):
"""
decorator for rename-like function, that need dispatch on 2 arguments
"""
def _wrapper_method(self, old_path, new_path):
old_path, _old_path, old_sentinel = _split_path(old_path);
new_path, _new_path, new_sentinel = _split_path(new_path);
if old_sentinel != new_sentinel:
raise ValueError('Does not know how to move things across contents manager mountpoints')
else:
sentinel = new_sentinel
|
python
|
{
"resource": ""
}
|
q2106
|
deactivate
|
train
|
def deactivate(profile='default'):
"""should be a matter of just unsetting the above keys
"""
with jconfig(profile) as config:
deact = True;
if not getattr(config.NotebookApp.contents_manager_class, 'startswith',lambda x:False)('jupyterdrive'):
|
python
|
{
"resource": ""
}
|
q2107
|
sequence_type
|
train
|
def sequence_type(seq):
'''Validates a coral.sequence data type.
:param sequence_in: input DNA sequence.
:type sequence_in: any
:returns: The material - 'dna', 'rna', or 'peptide'.
:rtype: str
:raises: ValueError
'''
if isinstance(seq, coral.DNA):
material = 'dna'
elif isinstance(seq, coral.RNA):
|
python
|
{
"resource": ""
}
|
q2108
|
digest
|
train
|
def digest(dna, restriction_enzyme):
'''Restriction endonuclease reaction.
:param dna: DNA template to digest.
:type dna: coral.DNA
:param restriction_site: Restriction site to use.
:type restriction_site: RestrictionSite
:returns: list of digested DNA fragments.
:rtype: coral.DNA list
'''
pattern = restriction_enzyme.recognition_site
located = dna.locate(pattern)
if not located[0] and not located[1]:
return [dna]
# Bottom strand indices are relative to the bottom strand 5' end.
# Convert to same type as top strand
pattern_len = len(pattern)
r_indices = [len(dna) - index - pattern_len for index in
located[1]]
# If sequence is palindrome, remove redundant results
if pattern.is_palindrome():
r_indices = [index for index in r_indices if
|
python
|
{
"resource": ""
}
|
q2109
|
_cut
|
train
|
def _cut(dna, index, restriction_enzyme):
'''Cuts template once at the specified index.
:param dna: DNA to cut
:type dna: coral.DNA
:param index: index at which to cut
:type index: int
:param restriction_enzyme: Enzyme with which to cut
:type restriction_enzyme: coral.RestrictionSite
:returns: 2-element list of digested sequence, including any overhangs.
:rtype: list
'''
# TODO: handle case where cut site is outside of recognition sequence,
# for both circular and linear cases where site is at index 0
# Find absolute indices at which to cut
cut_site = restriction_enzyme.cut_site
top_cut = index + cut_site[0]
bottom_cut = index + cut_site[1]
# Isolate left and ride sequences
to_cut = dna.pop()
max_cut = max(top_cut, bottom_cut)
min_cut = min(top_cut, bottom_cut)
left = to_cut[:max_cut]
|
python
|
{
"resource": ""
}
|
q2110
|
ipynb_to_rst
|
train
|
def ipynb_to_rst(directory, filename):
"""Converts a given file in a directory to an rst in the same directory."""
print(filename)
os.chdir(directory)
subprocess.Popen(["ipython", "nbconvert", "--to", "rst",
filename],
|
python
|
{
"resource": ""
}
|
q2111
|
convert_ipynbs
|
train
|
def convert_ipynbs(directory):
"""Recursively converts all ipynb files in a directory into rst files in
the same directory."""
# The ipython_examples dir has to be in the same dir as this script
for root, subfolders, files in os.walk(os.path.abspath(directory)):
|
python
|
{
"resource": ""
}
|
q2112
|
_context_walk
|
train
|
def _context_walk(dna, window_size, context_len, step):
'''Generate context-dependent 'non-boundedness' scores for a DNA sequence.
:param dna: Sequence to score.
:type dna: coral.DNA
:param window_size: Window size in base pairs.
:type window_size: int
:param context_len: The number of bases of context to use when analyzing
each window.
:type context_len: int
:param step: The number of base pairs to move for each new window.
:type step: int
'''
# Generate window indices
window_start_ceiling = len(dna) - context_len - window_size
window_starts = range(context_len - 1, window_start_ceiling, step)
window_ends = [start + window_size for start in window_starts]
# Generate left and right in-context subsequences
l_starts = [step * i for i in range(len(window_starts))]
l_seqs = [dna[start:end] for start, end in zip(l_starts, window_ends)]
r_ends = [x + window_size + context_len for x in window_starts]
r_seqs = [dna[start:end].reverse_complement() for start, end in
|
python
|
{
"resource": ""
}
|
q2113
|
StructureWindows.plot
|
train
|
def plot(self):
'''Plot the results of the run method.'''
try:
from matplotlib import pylab
except ImportError:
raise ImportError('Optional dependency matplotlib not installed.')
if self.walked:
fig = pylab.figure()
ax1 = fig.add_subplot(111)
|
python
|
{
"resource": ""
}
|
q2114
|
primer
|
train
|
def primer(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhang=None,
structure=False):
'''Design primer to a nearest-neighbor Tm setpoint.
:param dna: Sequence for which to design a primer.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters: Melting temp calculator method to use.
:type tm_parameters: string
:param overhang: Append the primer to this overhang sequence.
:type overhang: str
:param structure: Evaluate primer for structure, with warning for high
structure.
:type structure: bool
:returns: A primer.
:rtype: coral.Primer
:raises: ValueError if the input sequence is lower than the Tm settings
allow.
ValueError if a primer ending with G or C can't be found given
the Tm settings.
'''
# Check Tm of input sequence to see if it's already too low
seq_tm = coral.analysis.tm(dna, parameters=tm_parameters)
if seq_tm < (tm - tm_undershoot):
msg = 'Input sequence Tm is lower than primer Tm setting'
raise ValueError(msg)
# Focus on first 90 bases - shouldn't need more than 90bp to anneal
dna = dna[0:90]
# Generate primers from min_len to 'tm' + tm_overshoot
# TODO: this is a good place for optimization. Only calculate as many
# primers as are needed. Use binary search.
primers_tms = []
last_tm = 0
bases = min_len
while last_tm <= tm + tm_overshoot and bases != len(dna):
next_primer = dna[0:bases]
last_tm = coral.analysis.tm(next_primer, parameters=tm_parameters)
primers_tms.append((next_primer, last_tm))
bases += 1
# Trim primer list based on tm_undershoot and end_gc
primers_tms = [(primer, melt) for primer, melt in primers_tms if
melt >= tm - tm_undershoot]
if end_gc:
primers_tms = [pair for pair in primers_tms if
pair[0][-1] == coral.DNA('C') or
pair[0][-1] == coral.DNA('G')]
if not
|
python
|
{
"resource": ""
}
|
q2115
|
primers
|
train
|
def primers(dna, tm=65, min_len=10, tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning', overhangs=None,
structure=False):
'''Design primers for PCR amplifying any arbitrary sequence.
:param dna: Input sequence.
:type dna: coral.DNA
:param tm: Ideal primer Tm in degrees C.
:type tm: float
:param min_len: Minimum primer length.
:type min_len: int
:param tm_undershoot: Allowed Tm undershoot.
:type tm_undershoot: float
:param tm_overshoot: Allowed Tm overshoot.
:type tm_overshoot: float
:param end_gc: Obey the 'end on G or C' rule.
:type end_gc: bool
:param tm_parameters:
|
python
|
{
"resource": ""
}
|
q2116
|
Sanger.nonmatches
|
train
|
def nonmatches(self):
'''Report mismatches, indels, and coverage.'''
# For every result, keep a dictionary of mismatches, insertions, and
|
python
|
{
"resource": ""
}
|
q2117
|
Sanger.plot
|
train
|
def plot(self):
'''Make a summary plot of the alignment and highlight nonmatches.'''
import matplotlib.pyplot as plt
import matplotlib.patches as patches
# Constants to use throughout drawing
n = len(self.results)
nbases = len(self.aligned_reference)
barheight = 0.4
# Vary height of figure based on number of results
figheight = 3 + 3 * (n - 1)
fig = plt.figure(figsize=(9, figheight))
ax1 = fig.add_subplot(111)
# Plot bars to represent coverage area
# Reference sequence
ax1.add_patch(patches.Rectangle((0, 0), nbases, barheight,
facecolor='black'))
# Results
for i, report in enumerate(self.nonmatches()):
j = i + 1
start, stop = report['coverage']
patch = patches.Rectangle((start, j), stop - start, barheight,
facecolor='darkgray')
ax1.add_patch(patch)
# Draw a vertical line for each type of result
plt.vlines(report['mismatches'], j, j + barheight,
colors='b')
plt.vlines(report['insertions'], j, j + barheight,
|
python
|
{
"resource": ""
}
|
q2118
|
Sanger._remove_n
|
train
|
def _remove_n(self):
'''Remove terminal Ns from sequencing results.'''
for i, result in enumerate(self.results):
largest = max(str(result).split('N'),
|
python
|
{
"resource": ""
}
|
q2119
|
random_dna
|
train
|
def random_dna(n):
'''Generate a random DNA sequence.
:param n: Output sequence length.
:type n: int
:returns: Random DNA sequence of length n.
:rtype:
|
python
|
{
"resource": ""
}
|
q2120
|
random_codons
|
train
|
def random_codons(peptide, frequency_cutoff=0.0, weighted=False, table=None):
'''Generate randomized codons given a peptide sequence.
:param peptide: Peptide sequence for which to generate randomized
codons.
:type peptide: coral.Peptide
:param frequency_cutoff: Relative codon usage cutoff - codons that
are rarer will not be used. Frequency is
relative to average over all codons for a
given amino acid.
:param frequency_cutoff: Codon frequency table to use.
:param weighted: Use codon table
:type weighted: bool
:param table: Codon frequency table to use. Table should be organized
by amino acid, then be a dict of codon: frequency.
Only relevant if weighted=True or frequency_cutoff > 0.
Tables available:
constants.molecular_bio.CODON_FREQ_BY_AA['sc'] (default)
:type table: dict
:returns: Randomized sequence of codons (DNA) that code for the input
peptide.
:rtype: coral.DNA
:raises: ValueError if frequency_cutoff is set so high that there are no
codons available for an amino acid in the input peptide.
'''
if table is None:
table = CODON_FREQ_BY_AA['sc']
# Process codon table using frequency_cutoff
new_table = _cutoff(table, frequency_cutoff)
|
python
|
{
"resource": ""
}
|
q2121
|
_cutoff
|
train
|
def _cutoff(table, frequency_cutoff):
'''Generate new codon frequency table given a mean cutoff.
:param table: codon frequency table of form {amino acid: codon: frequency}
:type table: dict
:param frequency_cutoff: value between 0 and 1.0 for mean frequency cutoff
:type frequency_cutoff: float
:returns: A codon frequency table with some codons removed.
:rtype: dict
'''
new_table = {}
# IDEA: cutoff should be relative to
|
python
|
{
"resource": ""
}
|
q2122
|
fetch_genome
|
train
|
def fetch_genome(genome_id):
'''Acquire a genome from Entrez
'''
# TODO: Can strandedness by found in fetched genome attributes?
# TODO: skip read/write step?
# Using a dummy email for now - does this violate NCBI guidelines?
email = '[email protected]'
Entrez.email = email
print 'Downloading Genome...'
handle = Entrez.efetch(db='nucleotide', id=str(genome_id), rettype='gb',
|
python
|
{
"resource": ""
}
|
q2123
|
ViennaRNA.fold
|
train
|
def fold(self, strand, temp=37.0, dangles=2, nolp=False, nogu=False,
noclosinggu=False, constraints=None, canonicalbponly=False,
partition=False, pfscale=None, imfeelinglucky=False, gquad=False):
'''Run the RNAfold command and retrieve the result in a dictionary.
:param strand: The DNA or RNA sequence on which to run RNAfold.
:type strand: coral.DNA or coral.RNA
:param temp: Temperature at which to run the calculations.
:type temp: float
:param dangles: How to treat dangling end energies. Set to 0 to ignore
dangling ends. Set to 1 to limit unpaired bases to
at most one dangling end (default for MFE calc). Set to
2 (the default) to remove the limit in 1. Set to 3 to
allow coaxial stacking of adjacent helices in
.multi-loops
:type dangles: int
:param nolp: Produce structures without lonely pairs (isolated single
base pairs).
:type nolp: bool
:param nogu: Do not allow GU pairs.
:type nogu: bool
:param noclosinggu: Do not allow GU pairs at the end of helices.
:type noclosinggu: bool
:param constraints: Any structural constraints to use. Format is
defined at
http://www.tbi.univie.ac.at/RNA/RNAfold.1.html
:type constraints: str
:param canonicalbponly: Remove non-canonical base pairs from the
structure constraint (if applicable).
:type canonicalbponly: bool
:param partition: Generates the partition function, generating a coarse
grain structure ('coarse') in the format described at
http://www.itc.univie.ac.at/~ivo/RNA/RNAlib/PF-Fold.h
tml, the ensemble free energy ('ensemble'), the
centroid structure ('centroid'), the free energy of
|
python
|
{
"resource": ""
}
|
q2124
|
dimers
|
train
|
def dimers(primer1, primer2, concentrations=[5e-7, 3e-11]):
'''Calculate expected fraction of primer dimers.
:param primer1: Forward primer.
:type primer1: coral.DNA
:param primer2: Reverse primer.
:type primer2: coral.DNA
:param template: DNA template.
:type template: coral.DNA
:param concentrations: list of concentrations for primers and the
template. Defaults are those for PCR with 1kb
template.
:type concentrations: list
:returns: Fraction of dimers versus the total amount of primer added.
:rtype: float
'''
# It is not reasonable (yet) to use a long template for doing
|
python
|
{
"resource": ""
}
|
q2125
|
read_dna
|
train
|
def read_dna(path):
'''Read DNA from file. Uses BioPython and coerces to coral format.
:param path: Full path to input file.
:type path: str
:returns: DNA sequence.
:rtype: coral.DNA
'''
filename, ext = os.path.splitext(os.path.split(path)[-1])
genbank_exts = ['.gb', '.ape']
fasta_exts = ['.fasta', '.fa', '.fsa', '.seq']
abi_exts = ['.abi', '.ab1']
if any([ext == extension for extension in genbank_exts]):
file_format = 'genbank'
elif any([ext == extension for extension in fasta_exts]):
file_format = 'fasta'
elif any([ext == extension for
|
python
|
{
"resource": ""
}
|
q2126
|
_seqfeature_to_coral
|
train
|
def _seqfeature_to_coral(feature):
'''Convert a Biopython SeqFeature to a coral.Feature.
:param feature: Biopython SeqFeature
:type feature: Bio.SeqFeature
'''
# Some genomic sequences don't have a label attribute
# TODO: handle genomic cases differently than others. Some features lack
# a label but should still be incorporated somehow.
qualifiers = feature.qualifiers
if 'label' in qualifiers:
feature_name = qualifiers['label'][0]
elif 'locus_tag' in qualifiers:
feature_name = qualifiers['locus_tag'][0]
else:
raise FeatureNameError('Unrecognized feature name')
# Features with gaps are special, require looking at subfeatures
# Assumption: subfeatures are never more than one level deep
if feature.location_operator == 'join':
# Feature has gaps. Have to figure out start/stop from subfeatures,
# calculate gap indices. A nested feature model may be required
# eventually.
# Reorder the sub_feature list by start location
# Assumption: none of the subfeatures overlap so the last entry in
# the reordered list also has the final stop point of the feature.
# FIXME: Getting a deprecation warning about using sub_features
# instead of feature.location being a CompoundFeatureLocation
reordered = sorted(feature.location.parts,
key=lambda location: location.start)
starts = [int(location.start) for location in reordered]
stops = [int(location.end) for location in reordered]
feature_start = starts.pop(0)
|
python
|
{
"resource": ""
}
|
q2127
|
_coral_to_seqfeature
|
train
|
def _coral_to_seqfeature(feature):
'''Convert a coral.Feature to a Biopython SeqFeature.
:param feature: coral Feature.
:type feature: coral.Feature
'''
bio_strand = 1 if feature.strand == 1 else -1
ftype = _process_feature_type(feature.feature_type, bio_to_coral=False)
sublocations = []
if feature.gaps:
# There are gaps. Have to define location_operator and add subfeatures
location_operator = 'join'
# Feature location means nothing for 'join' sequences?
# TODO: verify
location = FeatureLocation(ExactPosition(0), ExactPosition(1),
strand=bio_strand)
# Reconstruct start/stop indices for each subfeature
stops, starts = zip(*feature.gaps)
starts = [feature.start] + [start + feature.start for start in starts]
stops = [stop + feature.start for stop in stops] + [feature.stop]
# Build subfeatures
for start, stop in zip(starts, stops):
sublocation = FeatureLocation(ExactPosition(start),
ExactPosition(stop),
|
python
|
{
"resource": ""
}
|
q2128
|
score_alignment
|
train
|
def score_alignment(a, b, gap_open, gap_extend, matrix):
'''Calculate the alignment score from two aligned sequences.
:param a: The first aligned sequence.
:type a: str
:param b: The second aligned sequence.
:type b: str
:param gap_open: The cost of opening a gap (negative number).
:type gap_open: int
:param gap_extend: The cost of extending an open gap (negative number).
:type gap_extend: int.
:param matrix: A score matrix dictionary name. Examples can be found in
the substitution_matrices module.
'''
al = a
bl = b
l = len(al)
|
python
|
{
"resource": ""
}
|
q2129
|
build_docs
|
train
|
def build_docs(directory):
"""Builds sphinx docs from a given directory."""
os.chdir(directory)
|
python
|
{
"resource": ""
}
|
q2130
|
gibson
|
train
|
def gibson(seq_list, circular=True, overlaps='mixed', overlap_tm=65,
maxlen=80, terminal_primers=True, primer_kwargs=None):
'''Design Gibson primers given a set of sequences
:param seq_list: List of DNA sequences to stitch together
:type seq_list: list containing coral.DNA
:param circular: If true, designs primers for making a circular construct.
If false, designs primers for a linear construct.
:type circular: bool
:param splits: Specifies locations of overlap. Must be either a single
entry of the same type as the 'split' parameter in
gibson_primers or a list of those types of the appropriate
length (for circular construct, len(seq_list), for
linear construct, len(seq_list) - 1)
:type splits: str or list of str
:param overlap_tm: Minimum Tm of overlap
:type overlap_tm: float
:param maxlen: Maximum length of each primer.
:type maxlen: int
:param terminal_primers: If the output is not circular, will design
non-Gibson primers for amplifying the first and
last fragments sans homology. If False, there will
be one less set of primers returned.
:type terminal_primers: bool
:param primer_kwargs: keyword arguments to pass to design.primer
:type primer_kwargs: dict
:returns: Forward and reverse primers for amplifying every fragment.
:rtype: a list of sequence.Primer tuples
:raises: ValueError if split parameter is an invalid string or wrong size.
'''
# Input checking
if circular:
n_overlaps = len(seq_list)
else:
n_overlaps = len(seq_list) - 1
if type(overlaps) is str:
overlaps = [overlaps] * n_overlaps
else:
if len(overlaps) != n_overlaps:
raise ValueError('Incorrect number of \'overlaps\' entries.')
else:
for overlap in overlaps:
if overlap not in ['left', 'right', 'mixed']:
raise ValueError('Invalid \'overlaps\' setting.')
if primer_kwargs is None:
primer_kwargs = {}
# If here, inputs were good
# Design primers for linear constructs:
primers_list = []
for i, (left, right) in enumerate(zip(seq_list[:-1], seq_list[1:])):
primers_list.append(gibson_primers(left, right, overlaps[i],
|
python
|
{
"resource": ""
}
|
q2131
|
reverse_complement
|
train
|
def reverse_complement(sequence, material):
'''Reverse complement a sequence.
:param sequence: Sequence to reverse complement
:type sequence: str
:param material: dna, rna, or peptide.
:type material: str
|
python
|
{
"resource": ""
}
|
q2132
|
check_alphabet
|
train
|
def check_alphabet(seq, material):
'''Verify that a given string is valid DNA, RNA, or peptide characters.
:param seq: DNA, RNA, or peptide sequence.
:type seq: str
:param material: Input material - 'dna', 'rna', or 'pepide'.
:type sequence: str
:returns: Whether the `seq` is a valid string of `material`.
:rtype: bool
:raises: ValueError if `material` isn't \'dna\', \'rna\', or \'peptide\'.
ValueError if `seq` contains invalid characters for its
material type.
'''
errs = {'dna': 'DNA', 'rna': 'RNA', 'peptide': 'peptide'}
if material == 'dna' or material == 'rna' or material == 'peptide':
alphabet = ALPHABETS[material]
err_msg
|
python
|
{
"resource": ""
}
|
q2133
|
process_seq
|
train
|
def process_seq(seq, material):
'''Validate and process sequence inputs.
:param seq: input sequence
:type seq: str
:param material: DNA, RNA, or peptide
:type: str
:returns: Uppercase version of `seq` with the alphabet checked by
|
python
|
{
"resource": ""
}
|
q2134
|
palindrome
|
train
|
def palindrome(seq):
'''Test whether a sequence is palindrome.
:param seq: Sequence to analyze (DNA or RNA).
:type seq: coral.DNA or coral.RNA
:returns: Whether a sequence is a palindrome.
:rtype: bool
'''
seq_len = len(seq)
if seq_len % 2 ==
|
python
|
{
"resource": ""
}
|
q2135
|
Feature.copy
|
train
|
def copy(self):
'''Return a copy of the Feature.
:returns: A safely editable copy of the current feature.
:rtype: coral.Feature
'''
return type(self)(self.name, self.start, self.stop, self.feature_type,
|
python
|
{
"resource": ""
}
|
q2136
|
nupack_multi
|
train
|
def nupack_multi(seqs, material, cmd, arguments, report=True):
'''Split Nupack commands over processors.
:param inputs: List of sequences, same format as for coral.analysis.Nupack.
:type inpus: list
:param material: Input material: 'dna' or 'rna'.
:type material: str
:param cmd: Command: 'mfe', 'pairs', 'complexes', or 'concentrations'.
:type cmd: str
:param arguments: Arguments for the command.
:type arguments: str
:returns: A list of the same return value you would get from `cmd`.
:rtype: list
'''
nupack_pool = multiprocessing.Pool()
try:
args = [{'seq': seq,
'cmd': cmd,
'material': material,
'arguments': arguments} for seq in seqs]
nupack_iterator = nupack_pool.imap(run_nupack, args)
total = len(seqs)
msg = ' calculations complete.'
passed = 4
while report:
completed =
|
python
|
{
"resource": ""
}
|
q2137
|
run_nupack
|
train
|
def run_nupack(kwargs):
'''Run picklable Nupack command.
:param kwargs: keyword arguments to pass to Nupack as well as 'cmd'.
:returns: Variable - whatever `cmd` returns.
'''
|
python
|
{
"resource": ""
}
|
q2138
|
NUPACK.pfunc_multi
|
train
|
def pfunc_multi(self, strands, permutation=None, temp=37.0, pseudo=False,
material=None, dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the partition function for an ordered complex of strands.
Runs the \'pfunc\' command.
:param strands: List of strands to use as inputs to pfunc -multi.
:type strands: list
:param permutation: The circular permutation of strands to test in
complex. e.g. to test in the order that was input
for 4 strands, the permutation would be [1,2,3,4].
If set to None, defaults to the order of the
input strands.
:type permutation: list
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
|
python
|
{
"resource": ""
}
|
q2139
|
NUPACK.subopt
|
train
|
def subopt(self, strand, gap, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Compute the suboptimal structures within a defined energy gap of the
MFE. Runs the \'subopt\' command.
:param strand: Strand on which to run subopt. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param gap: Energy gap within to restrict results, e.g. 0.1.
:type gap: float
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
'rna1999' for the RNA 1999 parameters.
:type material: str
:param dangles: How to treat dangles in the computation. From the
user guide: For \'none\': Dangle energies are ignored.
For \'some\': \'A dangle energy is incorporated for
each unpaired base flanking a duplex\'. For 'all': all
dangle energy is considered.
:type dangles: str
:param sodium: Sodium concentration in solution (molar), only applies
to DNA.
:type sodium: float
:param magnesium: Magnesium concentration in solution (molar), only
|
python
|
{
"resource": ""
}
|
q2140
|
NUPACK.energy
|
train
|
def energy(self, strand, dotparens, temp=37.0, pseudo=False, material=None,
dangles='some', sodium=1.0, magnesium=0.0):
'''Calculate the free energy of a given sequence structure. Runs the
\'energy\' command.
:param strand: Strand on which to run energy. Strands must be either
coral.DNA or coral.RNA).
:type strand: coral.DNA or coral.RNA
:param dotparens: The structure in dotparens notation.
:type dotparens: str
:param temp: Temperature setting for the computation. Negative values
are not allowed.
:type temp: float
:param pseudo: Enable pseudoknots.
:type pseudo: bool
:param material: The material setting to use in the computation. If set
to None (the default), the material type is inferred
from the strands. Other settings available: 'dna' for
DNA parameters, 'rna' for RNA (1995) parameters, and
|
python
|
{
"resource": ""
}
|
q2141
|
NUPACK.complexes_timeonly
|
train
|
def complexes_timeonly(self, strands, max_size):
'''Estimate the amount of time it will take to calculate all the
partition functions for each circular permutation - estimate the time
the actual \'complexes\' command will take to run.
:param strands: Strands on which to run energy. Strands must be either
coral.DNA or coral.RNA).
:type strands: list of coral.DNA or coral.RNA
:param max_size: Maximum complex size to consider (maximum number of
strand species in complex).
:type max_size: int
|
python
|
{
"resource": ""
}
|
q2142
|
NUPACK._multi_lines
|
train
|
def _multi_lines(self, strands, permutation):
'''Prepares lines to write to file for pfunc command input.
:param strand: Strand input (cr.DNA or cr.RNA).
:type strand: cr.DNA or cr.DNA
:param permutation: Permutation (e.g. [1, 2, 3, 4]) of the type used
by pfunc_multi.
:type permutation: list
'''
lines = []
# Write
|
python
|
{
"resource": ""
}
|
q2143
|
NUPACK._read_tempfile
|
train
|
def _read_tempfile(self, filename):
'''Read in and return file that's in the tempdir.
:param filename: Name of
|
python
|
{
"resource": ""
}
|
q2144
|
NUPACK._pairs_to_np
|
train
|
def _pairs_to_np(self, pairlist, dim):
'''Given a set of pair probability lines, construct a numpy array.
:param pairlist: a list of pair probability triples
:type pairlist: list
:returns: An upper triangular matrix of pair probabilities augmented
with one extra column that represents the unpaired
probabilities.
:rtype: numpy.array
'''
|
python
|
{
"resource": ""
}
|
q2145
|
_flip_feature
|
train
|
def _flip_feature(self, feature, parent_len):
'''Adjust a feature's location when flipping DNA.
:param feature: The feature to flip.
:type feature: coral.Feature
:param parent_len: The length of the sequence to which the feature belongs.
:type parent_len: int
|
python
|
{
"resource": ""
}
|
q2146
|
DNA.ape
|
train
|
def ape(self, ape_path=None):
'''Open in ApE if `ApE` is in your command line path.'''
# TODO: simplify - make ApE look in PATH only
cmd = 'ApE'
if ape_path is None:
# Check for ApE in PATH
ape_executables = []
for path in os.environ['PATH'].split(os.pathsep):
exepath = os.path.join(path, cmd)
ape_executables.append(os.access(exepath, os.X_OK))
if not any(ape_executables):
raise Exception('Ape not in PATH. Use ape_path kwarg.')
else:
cmd = ape_path
# Check whether ApE exists in PATH
|
python
|
{
"resource": ""
}
|
q2147
|
DNA.circularize
|
train
|
def circularize(self):
'''Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA
'''
if self.top[-1].seq == '-' and self.bottom[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
if self.bottom[-1].seq == '-' and self.top[0].seq == '-':
|
python
|
{
"resource": ""
}
|
q2148
|
DNA.flip
|
train
|
def flip(self):
'''Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA
'''
copy = self.copy()
|
python
|
{
"resource": ""
}
|
q2149
|
DNA.linearize
|
train
|
def linearize(self, index=0):
'''Linearize circular DNA at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.DNA
:raises: ValueError if the input
|
python
|
{
"resource": ""
}
|
q2150
|
DNA.locate
|
train
|
def locate(self, pattern):
'''Find sequences matching a pattern. For a circular sequence, the
search extends over the origin.
:param pattern: str or NucleicAcidSequence for which to find matches.
:type pattern: str or coral.DNA
:returns: A list of top and bottom strand indices
|
python
|
{
"resource": ""
}
|
q2151
|
DNA.reverse_complement
|
train
|
def reverse_complement(self):
'''Reverse complement the DNA.
:returns: A reverse-complemented instance of the current sequence.
:rtype: coral.DNA
'''
copy = self.copy()
# Note: if sequence is double-stranded,
|
python
|
{
"resource": ""
}
|
q2152
|
DNA.to_feature
|
train
|
def to_feature(self, name=None, feature_type='misc_feature'):
'''Create a feature from the current object.
:param name: Name for the new feature. Must be specified if the DNA
instance has no .name attribute.
:type name: str
:param feature_type: The type of feature (genbank standard).
:type feature_type: str
'''
if name is None:
if not self.name:
raise ValueError('name
|
python
|
{
"resource": ""
}
|
q2153
|
RestrictionSite.cuts_outside
|
train
|
def cuts_outside(self):
'''Report whether the enzyme cuts outside its recognition site.
Cutting at the very end of the site returns True.
:returns: Whether the enzyme will cut outside its recognition site.
:rtype: bool
'''
|
python
|
{
"resource": ""
}
|
q2154
|
Primer.copy
|
train
|
def copy(self):
'''Generate a Primer copy.
:returns: A safely-editable copy of the current primer.
:rtype: coral.DNA
|
python
|
{
"resource": ""
}
|
q2155
|
_pair_deltas
|
train
|
def _pair_deltas(seq, pars):
'''Add up nearest-neighbor parameters for a given sequence.
:param seq: DNA sequence for which to sum nearest neighbors
:type seq: str
:param pars: parameter set to use
:type pars: dict
:returns: nearest-neighbor delta_H and delta_S sums.
:rtype: tuple of floats
'''
delta0
|
python
|
{
"resource": ""
}
|
q2156
|
breslauer_corrections
|
train
|
def breslauer_corrections(seq, pars_error):
'''Sum corrections for Breslauer '84 method.
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtype: list of floats
'''
deltas_corr = [0, 0]
contains_gc = 'G' in str(seq) or 'C' in str(seq)
|
python
|
{
"resource": ""
}
|
q2157
|
MAFFT
|
train
|
def MAFFT(sequences, gap_open=1.53, gap_extension=0.0, retree=2):
'''A Coral wrapper for the MAFFT command line multiple sequence aligner.
:param sequences: A list of sequences to align.
:type sequences: List of homogeneous sequences (all DNA, or all RNA,
etc.)
:param gap_open: --op (gap open) penalty in MAFFT cli.
:type gap_open: float
:param gap_extension: --ep (gap extension) penalty in MAFFT cli.
:type gap_extension: float
:param retree: Number of times to build the guide tree.
:type retree: int
'''
arguments = ['mafft']
arguments += ['--op', str(gap_open)]
arguments += ['--ep', str(gap_extension)]
arguments += ['--retree', str(retree)]
arguments.append('input.fasta')
tempdir = tempfile.mkdtemp()
try:
with open(os.path.join(tempdir, 'input.fasta'), 'w') as f:
for i, sequence in enumerate(sequences):
if hasattr(sequence, 'name'):
name = sequence.name
else:
name = 'sequence{}'.format(i)
|
python
|
{
"resource": ""
}
|
q2158
|
repeats
|
train
|
def repeats(seq, size):
'''Count times that a sequence of a certain size is repeated.
:param seq: Input sequence.
:type seq: coral.DNA or coral.RNA
:param size: Size of the repeat to count.
:type size: int
:returns: Occurrences of repeats and how many
:rtype: tuple of the matched sequence and how many times it occurs
'''
seq = str(seq)
n_mers =
|
python
|
{
"resource": ""
}
|
q2159
|
gibson
|
train
|
def gibson(seq_list, linear=False, homology=10, tm=63.0):
'''Simulate a Gibson reaction.
:param seq_list: list of DNA sequences to Gibson
:type seq_list: list of coral.DNA
:param linear: Attempt to produce linear, rather than circular,
fragment from input fragments.
:type linear: bool
:param homology_min: minimum bp of homology allowed
:type homology_min: int
:param tm: Minimum tm of overlaps
:type tm: float
:returns: coral.reaction.Gibson instance.
:raises: ValueError if any input sequences are circular DNA.
'''
# FIXME: Preserve features in overlap
# TODO: set a max length?
# TODO: add 'expected' keyword argument somewhere to automate
# validation
# Remove any redundant (identical) sequences
seq_list = list(set(seq_list))
for seq in seq_list:
|
python
|
{
"resource": ""
}
|
q2160
|
_fuse_last
|
train
|
def _fuse_last(working_list, homology, tm):
'''With one sequence left, attempt to fuse it to itself.
:param homology: length of terminal homology in bp.
:type homology: int
:raises: AmbiguousGibsonError if either of the termini are palindromic
(would bind self-self).
ValueError if the ends are not compatible.
'''
# 1. Construct graph on self-self
# (destination, size, strand1, strand2)
pattern = working_list[0]
def graph_strands(strand1, strand2):
matchlen = homology_report(pattern, pattern, strand1, strand2,
cutoff=homology, min_tm=tm, top_two=True)
if matchlen:
# Ignore full-sequence matches
# HACK: modified homology_report to accept top_two. It should
# really just ignore full-length matches
for length in matchlen:
if length != len(pattern):
|
python
|
{
"resource": ""
}
|
q2161
|
get_gene_id
|
train
|
def get_gene_id(gene_name):
'''Retrieve systematic yeast gene name from the common name.
:param gene_name: Common name for yeast gene (e.g. ADE2).
:type gene_name: str
:returns: Systematic name for yeast gene (e.g. YOR128C).
:rtype: str
'''
from intermine.webservice import Service
service = Service('http://yeastmine.yeastgenome.org/yeastmine/service')
# Get a new query on the class (table) you will be querying:
query = service.new_query('Gene')
# The view specifies the output columns
query.add_view('primaryIdentifier', 'secondaryIdentifier', 'symbol',
'name', 'sgdAlias', 'crossReferences.identifier',
'crossReferences.source.name')
# Uncomment and edit the line below (the default) to select a custom sort
|
python
|
{
"resource": ""
}
|
q2162
|
_grow_overlaps
|
train
|
def _grow_overlaps(dna, melting_temp, require_even, length_max, overlap_min,
min_exception):
'''Grows equidistant overlaps until they meet specified constraints.
:param dna: Input sequence.
:type dna: coral.DNA
:param melting_temp: Ideal Tm of the overlaps, in degrees C.
:type melting_temp: float
:param require_even: Require that the number of oligonucleotides is even.
:type require_even: bool
:param length_max: Maximum oligo size (e.g. 60bp price point cutoff)
range.
:type length_range: int
:param overlap_min: Minimum overlap size.
:type overlap_min: int
:param min_exception: In order to meet melting_temp and overlap_min
settings, allow overlaps less than overlap_min to
continue growing above melting_temp.
:type min_exception: bool
:returns: Oligos, their overlapping regions, overlap Tms, and overlap
indices.
:rtype: tuple
'''
# TODO: prevent growing overlaps from bumping into each other -
# should halt when it happens, give warning, let user decide if they still
# want the current construct
# Another option would be to start over, moving the starting positions
# near the problem region a little farther from each other - this would
# put the AT-rich region in the middle of the spanning oligo
# Try bare minimum number of oligos
oligo_n = len(dna) // length_max + 1
# Adjust number of oligos if even number required
if require_even:
oligo_increment = 2
if oligo_n % 2 == 1:
oligo_n += 1
else:
oligo_increment = 1
# Increase oligo number until the minimum oligo_len is less than length_max
while float(len(dna)) / oligo_n > length_max:
oligo_n += oligo_increment
# Loop until all overlaps meet minimum Tm and length
tm_met = False
len_met = False
while(not tm_met or not len_met):
# Calculate initial number of overlaps
overlap_n = oligo_n - 1
# Place overlaps approximately equidistant over sequence length
overlap_interval = float(len(dna)) / oligo_n
starts = [int(overlap_interval * (i + 1)) for i in range(overlap_n)]
ends = [index + 1 for index in starts]
# Fencepost for while loop
# Initial overlaps (1 base) and their tms
overlaps = [dna[start:end] for start, end in zip(starts, ends)]
overlap_tms =
|
python
|
{
"resource": ""
}
|
q2163
|
_recalculate_overlaps
|
train
|
def _recalculate_overlaps(dna, overlaps, oligo_indices):
'''Recalculate overlap sequences based on the current overlap indices.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param overlaps: Current overlaps - a list of DNA sequences.
:type overlaps: coral.DNA list
:param oligo_indices: List of oligo indices (starts and stops).
:type oligo_indices: list
:returns: Overlap sequences.
:rtype: coral.DNA
|
python
|
{
"resource": ""
}
|
q2164
|
_expand_overlap
|
train
|
def _expand_overlap(dna, oligo_indices, index, oligos, length_max):
'''Given an overlap to increase, increases smaller oligo.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param oligo_indices: index of oligo starts and stops
:type oligo_indices: list
:param index: index of the oligo
:type index: int
:param left_len: length of left oligo
:type left_len: int
:param right_len: length of right oligo
:type right_len: int
:param length_max: length ceiling
:type length_max: int
:returns: New oligo list with one expanded.
:rtype: list
'''
left_len = len(oligos[index])
right_len = len(oligos[index + 1])
# If one of the oligos is max size, increase the other one
if right_len == length_max:
oligo_indices[1] = _adjust_overlap(oligo_indices[1],
|
python
|
{
"resource": ""
}
|
q2165
|
_adjust_overlap
|
train
|
def _adjust_overlap(positions_list, index, direction):
'''Increase overlap to the right or left of an index.
:param positions_list: list of overlap positions
:type positions_list: list
:param index: index of the overlap to increase.
:type index: int
:param direction: which side of the overlap to increase - left or right.
:type direction: str
:returns: A list of overlap positions (2-element lists)
:rtype: list
|
python
|
{
"resource": ""
}
|
q2166
|
OligoAssembly.design_assembly
|
train
|
def design_assembly(self):
'''Design the overlapping oligos.
:returns: Assembly oligos, and the sequences, Tms, and indices of their
overlapping regions.
:rtype: dict
'''
# Input parameters needed to design the oligos
length_range = self.kwargs['length_range']
oligo_number = self.kwargs['oligo_number']
require_even = self.kwargs['require_even']
melting_temp = self.kwargs['tm']
overlap_min = self.kwargs['overlap_min']
min_exception = self.kwargs['min_exception']
start_5 = self.kwargs['start_5']
if len(self.template) < length_range[0]:
# If sequence can be built with just two oligos, do that
oligos = [self.template, self.template.reverse_complement()]
overlaps = [self.template]
overlap_tms = [coral.analysis.tm(self.template)]
assembly_dict = {'oligos': oligos, 'overlaps': overlaps,
'overlap_tms': overlap_tms}
self.oligos = assembly_dict['oligos']
self.overlaps = assembly_dict['overlaps']
self.overlap_tms = assembly_dict['overlap_tms']
return assembly_dict
if oligo_number:
# Make first attempt using length_range[1] and see what happens
step = 3 # Decrease max range by this amount each iteration
length_max = length_range[1]
current_oligo_n = oligo_number + 1
oligo_n_met = False
above_min_len = length_max > length_range[0]
if oligo_n_met or not above_min_len:
raise Exception('Failed to design assembly.')
while not oligo_n_met and above_min_len:
# Starting with low range and going up doesnt work for longer
# sequence (overlaps become longer than 80)
assembly = _grow_overlaps(self.template, melting_temp,
require_even, length_max,
overlap_min, min_exception)
current_oligo_n = len(assembly[0])
if current_oligo_n > oligo_number:
break
|
python
|
{
"resource": ""
}
|
q2167
|
OligoAssembly.primers
|
train
|
def primers(self, tm=60):
'''Design primers for amplifying the assembled sequence.
:param tm: melting temperature (lower than overlaps is best).
|
python
|
{
"resource": ""
}
|
q2168
|
OligoAssembly.write_map
|
train
|
def write_map(self, path):
'''Write genbank map that highlights overlaps.
:param path: full path to .gb file to write.
:type path: str
'''
starts = [index[0] for index in self.overlap_indices]
features = []
for i, start in enumerate(starts):
stop = start + len(self.overlaps[i])
name = 'overlap {}'.format(i + 1)
feature_type = 'misc'
strand = 0
|
python
|
{
"resource": ""
}
|
q2169
|
coding_sequence
|
train
|
def coding_sequence(rna):
'''Extract coding sequence from an RNA template.
:param seq: Sequence from which to extract a coding sequence.
:type seq: coral.RNA
:param material: Type of sequence ('dna' or 'rna')
:type material: str
:returns: The first coding sequence (start codon -> stop codon) matched
from 5' to 3'.
:rtype: coral.RNA
:raises: ValueError if rna argument has no start codon.
ValueError if rna argument has no stop codon in-frame with the
first start codon.
'''
if isinstance(rna, coral.DNA):
|
python
|
{
"resource": ""
}
|
q2170
|
Rebase.update
|
train
|
def update(self):
'''Update definitions.'''
# Download http://rebase.neb.com/rebase/link_withref to tmp
self._tmpdir = tempfile.mkdtemp()
try:
self._rebase_file = self._tmpdir + '/rebase_file'
print 'Downloading latest enzyme definitions'
url = 'http://rebase.neb.com/rebase/link_withref'
header = {'User-Agent': 'Mozilla/5.0'}
req = urllib2.Request(url, headers=header)
con = urllib2.urlopen(req)
with open(self._rebase_file, 'wb') as rebase_file:
rebase_file.write(con.read())
# Process into self._enzyme_dict
self._process_file()
except urllib2.HTTPError, e:
print 'HTTP Error: {} {}'.format(e.code, url)
print 'Falling back on default enzyme list'
self._enzyme_dict = coral.constants.fallback_enzymes
except urllib2.URLError, e:
print 'URL Error: {} {}'.format(e.reason, url)
print 'Falling back on default enzyme list'
self._enzyme_dict = coral.constants.fallback_enzymes
# Process into RestrictionSite objects? (depends on speed)
print 'Processing into RestrictionSite instances.'
|
python
|
{
"resource": ""
}
|
q2171
|
Rebase._process_file
|
train
|
def _process_file(self):
'''Process rebase file into dict with name and cut site information.'''
print 'Processing file'
with open(self._rebase_file, 'r') as f:
raw = f.readlines()
names = [line.strip()[3:] for line in raw if line.startswith('<1>')]
seqs = [line.strip()[3:] for line in raw if line.startswith('<5>')]
if len(names) != len(seqs):
raise Exception('Found different number of enzyme names and '
'sequences.')
self._enzyme_dict = {}
for name, seq in zip(names, seqs):
if '?' in seq:
# Is unknown sequence, don't keep it
pass
elif seq.startswith('(') and seq.endswith(')'):
# Has four+ cut sites, don't keep it
pass
elif '^' in seq:
# Has reasonable internal cut sites, keep it
top_cut = seq.index('^')
|
python
|
{
"resource": ""
}
|
q2172
|
tempdir
|
train
|
def tempdir(fun):
'''For use as a decorator of instance methods - creates a temporary dir
named self._tempdir and then deletes it after the method runs.
:param fun: function to decorate
:type fun: instance method
'''
def wrapper(*args, **kwargs):
self = args[0]
|
python
|
{
"resource": ""
}
|
q2173
|
convert_sequence
|
train
|
def convert_sequence(seq, to_material):
'''Translate a DNA sequence into peptide sequence.
The following conversions are supported:
Transcription (seq is DNA, to_material is 'rna')
Reverse transcription (seq is RNA, to_material is 'dna')
Translation (seq is RNA, to_material is 'peptide')
:param seq: DNA or RNA sequence.
:type seq: coral.DNA or coral.RNA
:param to_material: material to which to convert ('rna', 'dna', or
'peptide').
:type to_material: str
:returns: sequence of type coral.sequence.[material type]
'''
if isinstance(seq, coral.DNA) and to_material == 'rna':
# Transcribe
# Can't transcribe a gap
if '-' in seq:
raise ValueError('Cannot transcribe gapped DNA')
# Convert DNA chars to RNA chars
origin = ALPHABETS['dna'][:-1]
destination = ALPHABETS['rna']
code = dict(zip(origin, destination))
converted = ''.join([code.get(str(k), str(k)) for k in seq])
# Instantiate RNA object
|
python
|
{
"resource": ""
}
|
q2174
|
NucleicAcid.gc
|
train
|
def gc(self):
'''Find the frequency of G and C in the current sequence.'''
|
python
|
{
"resource": ""
}
|
q2175
|
NucleicAcid.is_rotation
|
train
|
def is_rotation(self, other):
'''Determine whether two sequences are the same, just at different
rotations.
:param other: The sequence to check for rotational equality.
:type other: coral.sequence._sequence.Sequence
'''
if len(self) != len(other):
|
python
|
{
"resource": ""
}
|
q2176
|
NucleicAcid.linearize
|
train
|
def linearize(self, index=0):
'''Linearize the Sequence at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if the input is a linear sequence.
'''
if
|
python
|
{
"resource": ""
}
|
q2177
|
NucleicAcid.mw
|
train
|
def mw(self):
'''Calculate the molecular weight.
:returns: The molecular weight of the current sequence in amu.
:rtype: float
'''
counter = collections.Counter(self.seq.lower())
mw_a = counter['a'] * 313.2
mw_t = counter['t'] * 304.2
mw_g = counter['g'] *
|
python
|
{
"resource": ""
}
|
q2178
|
five_resect
|
train
|
def five_resect(dna, n_bases):
'''Remove bases from 5' end of top strand.
:param dna: Sequence to resect.
:type dna: coral.DNA
:param n_bases: Number of bases cut back.
:type n_bases: int
:returns: DNA sequence resected at the 5' end by n_bases.
:rtype: coral.DNA
'''
new_instance = dna.copy()
if n_bases >= len(dna):
|
python
|
{
"resource": ""
}
|
q2179
|
_remove_end_gaps
|
train
|
def _remove_end_gaps(sequence):
'''Removes double-stranded gaps from ends of the sequence.
:returns: The current sequence with terminal double-strand gaps ('-')
removed.
:rtype: coral.DNA
'''
# Count terminal blank sequences
def count_end_gaps(seq):
gap = coral.DNA('-')
count = 0
for base in seq:
if base == gap:
count += 1
else:
break
|
python
|
{
"resource": ""
}
|
q2180
|
needle
|
train
|
def needle(reference, query, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Do a Needleman-Wunsch alignment.
:param reference: Reference sequence.
:type reference: coral.DNA
:param query: Sequence to align against the reference.
:type query: coral.DNA
:param gapopen: Penalty for opening a gap.
:type gapopen: float
:param gapextend: Penalty for extending a gap.
:type gapextend: float
:param matrix: Matrix to use for alignment - options are DNA_simple (for
DNA) and BLOSUM62 (for proteins).
:type matrix: str
:returns: (aligned reference, aligned query, score)
:rtype: tuple of two coral.DNA instances and a float
'''
# Align using cython Needleman-Wunsch
aligned_ref, aligned_res = aligner(str(reference),
str(query),
gap_open=gap_open,
|
python
|
{
"resource": ""
}
|
q2181
|
needle_msa
|
train
|
def needle_msa(reference, results, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Create a multiple sequence alignment based on aligning every result
sequence against the reference, then inserting gaps until every aligned
reference is identical
'''
gap = '-'
# Convert alignments to list of strings
alignments = []
for result in results:
ref_dna, res_dna, score = needle(reference, result, gap_open=gap_open,
gap_extend=gap_extend,
matrix=matrix)
alignments.append([str(ref_dna), str(res_dna), score])
def insert_gap(sequence, position):
return sequence[:position] + gap + sequence[position:]
i = 0
while True:
# Iterate over 'columns' in every reference
refs = [alignment[0][i] for alignment in alignments]
# If there's a non-unanimous gap, insert gap into alignments
gaps = [ref == gap for ref in refs]
if any(gaps) and not all(gaps):
for alignment in alignments:
if alignment[0][i] != gap:
alignment[0] = insert_gap(alignment[0], i)
|
python
|
{
"resource": ""
}
|
q2182
|
needle_multi
|
train
|
def needle_multi(references, queries, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Batch process of sequencing split over several cores. Acts just like
needle but sequence inputs are lists.
:param references: References sequence.
:type references: coral.DNA list
:param queries: Sequences to align against the reference.
:type queries: coral.DNA list
:param gap_open: Penalty for opening a gap.
:type gap_open: float
:param gap_extend: Penalty for extending a gap.
:type gap_extend: float
:param matrix: Matrix to use for alignment - options are DNA_simple (for
DNA) and BLOSUM62 (for proteins).
:type matrix: str
:returns: a list of the same output as coral.sequence.needle
|
python
|
{
"resource": ""
}
|
q2183
|
import_global
|
train
|
def import_global(
name, modules=None, exceptions=DummyException, locals_=None,
globals_=None, level=-1):
'''Import the requested items into the global scope
WARNING! this method _will_ overwrite your global scope
If you have a variable named "path" and you call import_global('sys')
it will be overwritten with sys.path
Args:
name (str): the name of the module to import, e.g. sys
modules (str): the modules to import, use None for everything
exception (Exception): the exception to catch, e.g. ImportError
`locals_`: the `locals()` method (in case you need a different scope)
`globals_`: the `globals()` method (in case you need a different scope)
level (int): the level to import from, this can be used for
relative imports
'''
frame = None
try:
# If locals_ or globals_ are not given, autodetect them by inspecting
# the current stack
if locals_ is None or globals_ is None:
import inspect
frame = inspect.stack()[1][0]
if locals_ is None:
locals_ = frame.f_locals
if globals_ is None:
globals_ = frame.f_globals
try:
name = name.split('.')
# Relative imports are supported (from .spam import eggs)
if not name[0]:
name = name[1:]
level = 1
# raise IOError((name, level))
module = __import__(
name=name[0] or '.',
globals=globals_,
locals=locals_,
fromlist=name[1:],
level=max(level, 0),
|
python
|
{
"resource": ""
}
|
q2184
|
camel_to_underscore
|
train
|
def camel_to_underscore(name):
'''Convert camel case style naming to underscore style naming
If there are existing underscores they will be collapsed with the
to-be-added underscores. Multiple consecutive capital letters will not be
split except for the last one.
>>> camel_to_underscore('SpamEggsAndBacon')
'spam_eggs_and_bacon'
>>> camel_to_underscore('Spam_and_bacon')
'spam_and_bacon'
>>> camel_to_underscore('Spam_And_Bacon')
'spam_and_bacon'
>>> camel_to_underscore('__SpamAndBacon__')
'__spam_and_bacon__'
|
python
|
{
"resource": ""
}
|
q2185
|
timedelta_to_seconds
|
train
|
def timedelta_to_seconds(delta):
'''Convert a timedelta to seconds with the microseconds as fraction
Note that this method has become largely obsolete with the
`timedelta.total_seconds()` method introduced in Python 2.7.
>>> from datetime import timedelta
>>> '%d' % timedelta_to_seconds(timedelta(days=1))
'86400'
>>> '%d' % timedelta_to_seconds(timedelta(seconds=1))
'1'
>>> '%.6f' % timedelta_to_seconds(timedelta(seconds=1, microseconds=1))
'1.000001'
|
python
|
{
"resource": ""
}
|
q2186
|
get_terminal_size
|
train
|
def get_terminal_size(): # pragma: no cover
'''Get the current size of your terminal
Multiple returns are not always a good idea, but in this case it greatly
simplifies the code so I believe it's justified. It's not the prettiest
function but that's never really possible with cross-platform code.
Returns:
width, height: Two integers containing width and height
'''
try:
# Default to 79 characters for IPython notebooks
from IPython import get_ipython
ipython = get_ipython()
from ipykernel import zmqshell
if isinstance(ipython, zmqshell.ZMQInteractiveShell):
return 79, 24
except Exception: # pragma: no cover
pass
try:
# This works for Python 3, but not Pypy3. Probably the best method if
# it's supported so let's always try
import shutil
w, h = shutil.get_terminal_size()
|
python
|
{
"resource": ""
}
|
q2187
|
Skype.AsyncSearchUsers
|
train
|
def AsyncSearchUsers(self, Target):
"""Asynchronously searches for Skype users.
:Parameters:
Target : unicode
Search target (name or email address).
:return: A search identifier. It will be passed along with the results to the
`SkypeEvents.AsyncSearchUsersFinished` event after the search is completed.
|
python
|
{
"resource": ""
}
|
q2188
|
Skype.Attach
|
train
|
def Attach(self, Protocol=5, Wait=True):
"""Establishes a connection to Skype.
:Parameters:
Protocol : int
Minimal Skype protocol version.
Wait : bool
If set to False, blocks forever until the connection is established. Otherwise, timeouts
after the `Timeout`.
|
python
|
{
"resource": ""
}
|
q2189
|
Skype.Call
|
train
|
def Call(self, Id=0):
"""Queries a call object.
:Parameters:
Id : int
Call identifier.
|
python
|
{
"resource": ""
}
|
q2190
|
Skype.ChangeUserStatus
|
train
|
def ChangeUserStatus(self, Status):
"""Changes the online status for the current user.
:Parameters:
Status : `enums`.cus*
New online status for the user.
:note: This function waits until the online status changes. Alternatively, use the
`CurrentUserStatus` property to perform an immediate change of status.
|
python
|
{
"resource": ""
}
|
q2191
|
Skype.Chat
|
train
|
def Chat(self, Name=''):
"""Queries a chat object.
:Parameters:
Name : str
Chat name.
:return: A chat object.
:rtype: `chat.Chat`
"""
|
python
|
{
"resource": ""
}
|
q2192
|
Skype.ClearCallHistory
|
train
|
def ClearCallHistory(self, Username='ALL', Type=chsAllCalls):
"""Clears the call history.
:Parameters:
Username : str
Skypename of the user. A special value of 'ALL' means that entries of all users should
be removed.
|
python
|
{
"resource": ""
}
|
q2193
|
Skype.Command
|
train
|
def Command(self, Command, Reply=u'', Block=False, Timeout=30000, Id=-1):
"""Creates an API command object.
:Parameters:
Command : unicode
Command string.
Reply : unicode
Expected reply. By default any reply is accepted (except errors which raise an
`SkypeError` exception).
Block : bool
If set to True, `SendCommand` method waits for a response from Skype API before
returning.
Timeout : float, int or long
Timeout. Used if Block == True. Timeout may be expressed in milliseconds if the type
|
python
|
{
"resource": ""
}
|
q2194
|
Skype.Conference
|
train
|
def Conference(self, Id=0):
"""Queries a call conference object.
:Parameters:
Id : int
Conference Id.
:return: A conference object.
:rtype: `Conference`
"""
|
python
|
{
"resource": ""
}
|
q2195
|
Skype.CreateChatWith
|
train
|
def CreateChatWith(self, *Usernames):
"""Creates a chat with one or more users.
:Parameters:
Usernames : str
One or more Skypenames of the users.
:return: A chat object
:rtype: `Chat`
|
python
|
{
"resource": ""
}
|
q2196
|
Skype.CreateGroup
|
train
|
def CreateGroup(self, GroupName):
"""Creates a custom contact group.
:Parameters:
GroupName : unicode
Group name.
:return: A group object.
:rtype: `Group`
:see: `DeleteGroup`
"""
groups = self.CustomGroups
|
python
|
{
"resource": ""
}
|
q2197
|
Skype.CreateSms
|
train
|
def CreateSms(self, MessageType, *TargetNumbers):
"""Creates an SMS message.
:Parameters:
MessageType : `enums`.smsMessageType*
Message type.
TargetNumbers : str
One or more target SMS numbers.
|
python
|
{
"resource": ""
}
|
q2198
|
Skype.Greeting
|
train
|
def Greeting(self, Username=''):
"""Queries the greeting used as voicemail.
:Parameters:
Username : str
Skypename of the user.
:return: A voicemail object.
:rtype: `Voicemail`
"""
for v in self.Voicemails:
|
python
|
{
"resource": ""
}
|
q2199
|
Skype.Message
|
train
|
def Message(self, Id=0):
"""Queries a chat message object.
:Parameters:
Id : int
Message Id.
:return: A chat message object.
:rtype: `ChatMessage`
"""
|
python
|
{
"resource": ""
}
|
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