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acutesoftware/AIKIF | aikif/lib/cls_file.py | TextFile.count_lines_in_file | def count_lines_in_file(self, fname=''):
""" you wont believe what this method does """
i = 0
if fname == '':
fname = self.fullname
try:
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with codecs.open(fname, "r",encoding='utf8', errors='ignore') as f:
... | python | def count_lines_in_file(self, fname=''):
""" you wont believe what this method does """
i = 0
if fname == '':
fname = self.fullname
try:
#with open(fname, encoding="utf8") as f:
with codecs.open(fname, "r",encoding='utf8', errors='ignore') as f:
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acutesoftware/AIKIF | aikif/lib/cls_file.py | TextFile.count_lines_of_code | def count_lines_of_code(self, fname=''):
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""" counts non blank lines """
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acutesoftware/AIKIF | aikif/lib/cls_file.py | TextFile.get_file_sample | def get_file_sample(self, numLines=10):
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res += str(line_num).zfill(5) + ' ' + line
if line_num >= numLi... | python | def get_file_sample(self, numLines=10):
""" retrieve a sample of the file """
res = ''
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acutesoftware/AIKIF | aikif/lib/cls_file.py | TextFile.append_text | def append_text(self, txt):
""" adds a line of text to a file """
with open(self.fullname, "a") as myfile:
myfile.write(txt) | python | def append_text(self, txt):
""" adds a line of text to a file """
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acutesoftware/AIKIF | aikif/lib/cls_file.py | TextFile.load_file_to_string | def load_file_to_string(self):
""" load a file to a string """
try:
with open(self.fullname, 'r') as f:
txt = f.read()
return txt
except IOError:
return '' | python | def load_file_to_string(self):
""" load a file to a string """
try:
with open(self.fullname, 'r') as f:
txt = f.read()
return txt
except IOError:
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acutesoftware/AIKIF | aikif/lib/cls_file.py | TextFile.load_file_to_list | def load_file_to_list(self):
""" load a file to a list """
lst = []
try:
with open(self.fullname, 'r') as f:
for line in f:
lst.append(line)
return lst
except IOError:
return lst | python | def load_file_to_list(self):
""" load a file to a list """
lst = []
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for line in f:
lst.append(line)
return lst
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acutesoftware/AIKIF | aikif/web_app/page_programs.py | get_program_list | def get_program_list():
"""
get a HTML formatted view of all Python programs
in all subfolders of AIKIF, including imports and
lists of functions and classes
"""
colList = ['FileName','FileSize','Functions', 'Imports']
txt = '<TABLE width=90% border=0>'
txt += format_file_table_header(c... | python | def get_program_list():
"""
get a HTML formatted view of all Python programs
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"""
colList = ['FileName','FileSize','Functions', 'Imports']
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acutesoftware/AIKIF | aikif/web_app/page_programs.py | get_subfolder | def get_subfolder(txt):
"""
extracts a displayable subfolder name from full filename
"""
root_folder = os.sep + 'aikif' + os.sep
ndx = txt.find(root_folder, 1)
return txt[ndx:].replace('__init__.py', '') | python | def get_subfolder(txt):
"""
extracts a displayable subfolder name from full filename
"""
root_folder = os.sep + 'aikif' + os.sep
ndx = txt.find(root_folder, 1)
return txt[ndx:].replace('__init__.py', '') | [
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acutesoftware/AIKIF | aikif/web_app/page_programs.py | get_functions | def get_functions(fname):
""" get a list of functions from a Python program """
txt = ''
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txt += '<PRE>' + strip_text_after_string(strip_text_after_string(line, '#')[4:], ':') + '</PRE>\n'
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""" get a list of functions from a Python program """
txt = ''
with open(fname, 'r') as f:
for line in f:
if line.strip()[0:4] == 'def ':
txt += '<PRE>' + strip_text_after_string(strip_text_after_string(line, '#')[4:], ':') + '</PRE>\n'
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acutesoftware/AIKIF | aikif/web_app/page_programs.py | strip_text_after_string | def strip_text_after_string(txt, junk):
""" used to strip any poorly documented comments at the end of function defs """
if junk in txt:
return txt[:txt.find(junk)]
else:
return txt | python | def strip_text_after_string(txt, junk):
""" used to strip any poorly documented comments at the end of function defs """
if junk in txt:
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else:
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acutesoftware/AIKIF | aikif/web_app/page_programs.py | get_imports | def get_imports(fname):
""" get a list of imports from a Python program """
txt = ''
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txt += '<PRE>' + strip_text_after_string(line[7:], ' as ') + '</PRE>\n'
return txt + '<BR>' | python | def get_imports(fname):
""" get a list of imports from a Python program """
txt = ''
with open(fname, 'r') as f:
for line in f:
if line[0:6] == 'import':
txt += '<PRE>' + strip_text_after_string(line[7:], ' as ') + '</PRE>\n'
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acutesoftware/AIKIF | aikif/agents/learn/dummy_learn_1.py | main | def main(arg1=55, arg2='test', arg3=None):
"""
This is a sample program to show how a learning agent can
be logged using AIKIF.
The idea is that this main function is your algorithm, which
will run until it finds a successful result. The result is
returned and the time taken is logged.
... | python | def main(arg1=55, arg2='test', arg3=None):
"""
This is a sample program to show how a learning agent can
be logged using AIKIF.
The idea is that this main function is your algorithm, which
will run until it finds a successful result. The result is
returned and the time taken is logged.
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acutesoftware/AIKIF | aikif/dataTools/if_redis.py | redis_server.get | def get(self, key):
""" get a set of keys from redis """
res = self.connection.get(key)
print(res)
return res | python | def get(self, key):
""" get a set of keys from redis """
res = self.connection.get(key)
print(res)
return res | [
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Nachtfeuer/pipeline | spline/components/packer.py | Packer.creator | def creator(_, config):
"""Creator function for creating an instance of a Packer image script."""
packer_script = render(config.script, model=config.model, env=config.env,
variables=config.variables, item=config.item)
filename = "packer.dry.run.see.comment"
... | python | def creator(_, config):
"""Creator function for creating an instance of a Packer image script."""
packer_script = render(config.script, model=config.model, env=config.env,
variables=config.variables, item=config.item)
filename = "packer.dry.run.see.comment"
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wanadev/pyguetzli | pyguetzli/guetzli.py | process_jpeg_bytes | def process_jpeg_bytes(bytes_in, quality=DEFAULT_JPEG_QUALITY):
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:param bytes_in: the input image's bytes
:param quality: the output JPEG quality (default 95)
:returns: Optimized JPEG bytes
:rtype: bytes
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"""Generates an optimized JPEG from JPEG-encoded bytes.
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:param quality: the output JPEG quality (default 95)
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wanadev/pyguetzli | pyguetzli/guetzli.py | process_rgb_bytes | def process_rgb_bytes(bytes_in, width, height, quality=DEFAULT_JPEG_QUALITY):
"""Generates an optimized JPEG from RGB bytes.
:param bytes bytes_in: the input image's bytes
:param int width: the width of the input image
:param int height: the height of the input image
:param int quality: the output ... | python | def process_rgb_bytes(bytes_in, width, height, quality=DEFAULT_JPEG_QUALITY):
"""Generates an optimized JPEG from RGB bytes.
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Nachtfeuer/pipeline | spline/tools/decorators.py | singleton | def singleton(the_class):
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"""
Decorator for a class to make a singleton out of it.
@type the_class: class
@param the_class: the class that should work as a singleton
@rtype: decorator
@return: decorator
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""" builds a 2048 starting board
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grd = Grid(4,4, [2,4])
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acutesoftware/AIKIF | aikif/toolbox/game_board_utils.py | TEST | def TEST():
""" tests for this module """
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grd.new_tile()
grd.new_tile()
print(grd)
print("There are ", grd.count_blank_positions(), " blanks in grid 1\n")
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grd2.new_tile(26)
print(grd2)
build_board_checkers()
print("There ar... | python | def TEST():
""" tests for this module """
grd = Grid(4,4, [2,4])
grd.new_tile()
grd.new_tile()
print(grd)
print("There are ", grd.count_blank_positions(), " blanks in grid 1\n")
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Ask blobstore api for an url to directly serve the file
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budacom/trading-bots | trading_bots/contrib/clients.py | MarketClient.fetch_order_book | def fetch_order_book(self) -> OrderBook:
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budacom/trading-bots | trading_bots/contrib/clients.py | MarketClient.fetch_trades_since | def fetch_trades_since(self, since: int) -> List[Trade]:
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budacom/trading-bots | trading_bots/contrib/clients.py | WalletClient.fetch_deposits | def fetch_deposits(self, limit: int) -> List[Deposit]:
"""Fetch latest deposits, must provide a limit."""
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budacom/trading-bots | trading_bots/contrib/clients.py | WalletClient.fetch_withdrawals | def fetch_withdrawals(self, limit: int) -> List[Withdrawal]:
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budacom/trading-bots | trading_bots/contrib/clients.py | WalletClient.fetch_withdrawals_since | def fetch_withdrawals_since(self, since: int) -> List[Withdrawal]:
"""Fetch all withdrawals since the given timestamp."""
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budacom/trading-bots | trading_bots/contrib/clients.py | WalletClient.request_withdrawal | def request_withdrawal(self, amount: Number, address: str, subtract_fee: bool=False, **params) -> Withdrawal:
"""Request a withdrawal."""
self.log.debug(f'Requesting {self.currency} withdrawal from {self.name} to {address}')
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"""Request a withdrawal."""
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budacom/trading-bots | trading_bots/contrib/clients.py | TradingClient.fetch_order | def fetch_order(self, order_id: str) -> Order:
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budacom/trading-bots | trading_bots/contrib/clients.py | TradingClient.fetch_closed_orders_since | def fetch_closed_orders_since(self, since: int) -> List[Order]:
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budacom/trading-bots | trading_bots/contrib/clients.py | TradingClient.cancel_order | def cancel_order(self, order_id: str) -> str:
"""Cancel an order by ID."""
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"""Cancel an order by ID."""
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budacom/trading-bots | trading_bots/contrib/clients.py | TradingClient.cancel_orders | def cancel_orders(self, order_ids: List[str]) -> List[str]:
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budacom/trading-bots | trading_bots/contrib/clients.py | TradingClient.cancel_all_orders | def cancel_all_orders(self) -> List[str]:
"""Cancel all open orders."""
order_ids = [o.id for o in self.fetch_all_open_orders()]
return self.cancel_orders(order_ids) | python | def cancel_all_orders(self) -> List[str]:
"""Cancel all open orders."""
order_ids = [o.id for o in self.fetch_all_open_orders()]
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budacom/trading-bots | trading_bots/contrib/clients.py | TradingClient.min_order_amount | def min_order_amount(self) -> Money:
"""Minimum amount to place an order."""
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"""Minimum amount to place an order."""
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budacom/trading-bots | trading_bots/contrib/clients.py | TradingClient.place_market_order | def place_market_order(self, side: Side, amount: Number) -> Order:
"""Place a market order."""
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BD2KGenomics/protect | attic/encrypt_files_in_dir_to_s3.py | main | def main():
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Queries S3 to identify the region hosting the provided bucket.
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# TODO: Make the bucket here?
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Queries S3 to identify the region hosting the provided bucket.
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BD2KGenomics/protect | src/protect/alignment/rna.py | align_rna | def align_rna(job, fastqs, univ_options, star_options):
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A wrapper for the entire rna alignment subgraph.
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drslump/pyshould | pyshould/expectation.py | Expectation.reset | def reset(self):
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"""
matcher = lookup(alias)
if not matcher:
msg = 'Matcher "%s" not found' % alias
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""" Finds a matcher based on the given alias or raises an error if no
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drslump/pyshould | pyshould/expectation.py | Expectation._init_matcher | def _init_matcher(self, *args, **kwargs):
""" Executes the current matcher appending it to the expression """
# If subject-less expectation are provided as arguments convert them
# to plain Hamcrest matchers in order to allow complex compositions
fn = lambda x: x.evaluate() if isinstanc... | python | def _init_matcher(self, *args, **kwargs):
""" Executes the current matcher appending it to the expression """
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""" Specify a custom message for the matcher """
if len(args):
description = description.format(*args)
self.description = description
return self | python | def described_as(self, description, *args):
""" Specify a custom message for the matcher """
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bkg/django-spillway | spillway/carto.py | make_dbsource | def make_dbsource(**kwargs):
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return mapnik.SQLite(wkb_format='spatialite', **kwargs)
names = (('dbname', 'NAME'), ('user... | python | def make_dbsource(**kwargs):
"""Returns a mapnik PostGIS or SQLite Datasource."""
if 'spatialite' in connection.settings_dict.get('ENGINE'):
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queryset -- QuerySet for Layer
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stylename -- str name of style to apply
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cls = RasterLayer if hasattr(queryset, 'image') else VectorLayer
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queryset -- QuerySet for Layer
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stylename -- str name of style to apply
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bkg/django-spillway | spillway/carto.py | Map.zoom_bbox | def zoom_bbox(self, bbox):
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bbox -- OGRGeometry polygon to zoom map extent
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BD2KGenomics/protect | src/protect/mutation_calling/fusion.py | wrap_fusion | def wrap_fusion(job,
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"""
A wrapper for run_fusion using the results from cutadapt and star as input.
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BD2KGenomics/protect | src/protect/mutation_calling/fusion.py | parse_star_fusion | def parse_star_fusion(infile):
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:param str infile: path to STAR-Fusion prediction file
:return: Fusion prediction attributes
:rtype: bd2k.util.expando.Expando
"""
reader = csv.reader(infile, delimiter='\t')
h... | python | def parse_star_fusion(infile):
"""
Parses STAR-Fusion format and returns an Expando object with basic features
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BD2KGenomics/protect | src/protect/mutation_calling/fusion.py | get_transcripts | def get_transcripts(transcript_file):
"""
Parses FusionInspector transcript file and returns dictionary of sequences
:param str transcript_file: path to transcript FASTA
:return: de novo assembled transcripts
:rtype: dict
"""
with open(transcript_file, 'r') as fa:
transcripts = {}
... | python | def get_transcripts(transcript_file):
"""
Parses FusionInspector transcript file and returns dictionary of sequences
:param str transcript_file: path to transcript FASTA
:return: de novo assembled transcripts
:rtype: dict
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BD2KGenomics/protect | src/protect/mutation_calling/fusion.py | split_fusion_transcript | def split_fusion_transcript(annotation_path, transcripts):
"""
Finds the breakpoint in the fusion transcript and splits the 5' donor from the 3' acceptor
:param str annotation_path: Path to transcript annotation file
:param dict transcripts: Dictionary of fusion transcripts
:return: 5' donor sequen... | python | def split_fusion_transcript(annotation_path, transcripts):
"""
Finds the breakpoint in the fusion transcript and splits the 5' donor from the 3' acceptor
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BD2KGenomics/protect | src/protect/mutation_calling/fusion.py | get_gene_ids | def get_gene_ids(fusion_bed):
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Parses FusionInspector bed file to ascertain the ENSEMBL gene ids
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:return: dict
"""
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for line in f:... | python | def get_gene_ids(fusion_bed):
"""
Parses FusionInspector bed file to ascertain the ENSEMBL gene ids
:param str fusion_bed: path to fusion annotation
:return: dict
"""
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regex = re.compile(r'(?P<gene>ENSG\d*)')
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BD2KGenomics/protect | src/protect/mutation_calling/fusion.py | reformat_star_fusion_output | def reformat_star_fusion_output(job,
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | get_fastq_2 | def get_fastq_2(job, patient_id, sample_type, fastq_1):
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For a path to a fastq_1 file, return a fastq_2 file with the same prefix and naming scheme.
:param str patient_id: The patient_id
:param str sample_type: The sample type of the file
:param str fastq_1: The path to the fastq_1 file
:ret... | python | def get_fastq_2(job, patient_id, sample_type, fastq_1):
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | parse_config_file | def parse_config_file(job, config_file, max_cores=None):
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Parse the config file and spawn a ProTECT job for every input sample.
:param str config_file: Path to the input config file
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sample_set, univ_options, ... | python | def parse_config_file(job, config_file, max_cores=None):
"""
Parse the config file and spawn a ProTECT job for every input sample.
:param str config_file: Path to the input config file
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | get_all_tool_inputs | def get_all_tool_inputs(job, tools, outer_key='', mutation_caller_list=None):
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | get_pipeline_inputs | def get_pipeline_inputs(job, input_flag, input_file, encryption_key=None, per_file_encryption=False,
gdc_download_token=None):
"""
Get the input file from s3 or disk and write to file store.
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | prepare_samples | def prepare_samples(job, patient_dict, univ_options):
"""
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|- 'tumor_dna_fastq_[12]' OR 'tumor_dna_bam': str
|- 'tumor_rna_fastq_[12]... | python | def prepare_samples(job, patient_dict, univ_options):
"""
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | get_patient_bams | def get_patient_bams(job, patient_dict, sample_type, univ_options, bwa_options, mutect_options):
"""
Convenience function to return the bam and its index in the correct format for a sample type.
:param dict patient_dict: dict of patient info
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | get_patient_vcf | def get_patient_vcf(job, patient_dict):
"""
Convenience function to get the vcf from the patient dict
:param dict patient_dict: dict of patient info
:return: The vcf
:rtype: toil.fileStore.FileID
"""
temp = job.fileStore.readGlobalFile(patient_dict['mutation_vcf'],
... | python | def get_patient_vcf(job, patient_dict):
"""
Convenience function to get the vcf from the patient dict
:param dict patient_dict: dict of patient info
:return: The vcf
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | get_patient_mhc_haplotype | def get_patient_mhc_haplotype(job, patient_dict):
"""
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:param dict patient_dict: dict of patient info
:return: The MHCI and MHCII haplotypes
:rtype: toil.fileStore.FileID
"""
haplotype_archive = job.fileStore.readGlobalFile(... | python | def get_patient_mhc_haplotype(job, patient_dict):
"""
Convenience function to get the mhc haplotype from the patient dict
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | get_patient_expression | def get_patient_expression(job, patient_dict):
"""
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:param dict patient_dict: dict of patient info
:return: The gene and isoform expression
:rtype: toil.fileStore.FileID
"""
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"""
Convenience function to get the expression from the patient dict
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BD2KGenomics/protect | src/protect/pipeline/ProTECT.py | generate_config_file | def generate_config_file():
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"""
Generate a config file for a ProTECT run on hg19.
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Run snpeff on an input vcf.
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Run snpeff on an input vcf.
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A wrapper for the entire dna alignment subgraph.
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Align a pair of fastqs with bwa.
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Fix the bam header to remove the command line call. Failing to do this causes Picard to reject
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Add read groups to the bam.
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nepalicalendar/nepalicalendar-py | nepalicalendar/nepcal.py | NepCal.itermonthdays | def itermonthdays(cls, year, month):
"""Similar to itermonthdates but returns day number instead of NepDate object
"""
for day in NepCal.itermonthdates(year, month):
if day.month == month:
yield day.day
else:
yield 0 | python | def itermonthdays(cls, year, month):
"""Similar to itermonthdates but returns day number instead of NepDate object
"""
for day in NepCal.itermonthdates(year, month):
if day.month == month:
yield day.day
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nepalicalendar/nepalicalendar-py | nepalicalendar/nepcal.py | NepCal.itermonthdays2 | def itermonthdays2(cls, year, month):
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"""Similar to itermonthdays2 but returns tuples of day and weekday.
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for day in NepCal.itermonthdates(year, month):
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nepalicalendar/nepalicalendar-py | nepalicalendar/nepcal.py | NepCal.monthdatescalendar | def monthdatescalendar(cls, year, month):
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""" Returns a list of week in a month. A week is a list of NepDate objects """
weeks = []
week = []
for day in NepCal.itermonthdates(year, month):
week.append(day)
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nepalicalendar/nepalicalendar-py | nepalicalendar/nepcal.py | NepCal.monthdayscalendar | def monthdayscalendar(cls, year, month):
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weeks = []
week = []
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nepalicalendar/nepalicalendar-py | nepalicalendar/nepcal.py | NepCal.monthdays2calendar | def monthdays2calendar(cls, year, month):
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weeks = []
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for day in NepCal.itermonthdays2(year, month):
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""" Return a list of the weeks in the month month of the year as full weeks.
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BD2KGenomics/protect | src/protect/mutation_calling/somaticsniper.py | run_somaticsniper_with_merge | def run_somaticsniper_with_merge(job, tumor_bam, normal_bam, univ_options, somaticsniper_options):
"""
A wrapper for the the entire SomaticSniper sub-graph.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
:param dict normal_bam: Dict of bam and bai for normal DNA-Seq
:param dict univ_o... | python | def run_somaticsniper_with_merge(job, tumor_bam, normal_bam, univ_options, somaticsniper_options):
"""
A wrapper for the the entire SomaticSniper sub-graph.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
:param dict normal_bam: Dict of bam and bai for normal DNA-Seq
:param dict univ_o... | [
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BD2KGenomics/protect | src/protect/mutation_calling/somaticsniper.py | run_somaticsniper | def run_somaticsniper(job, tumor_bam, normal_bam, univ_options, somaticsniper_options, split=True):
"""
Run the SomaticSniper subgraph on the DNA bams. Optionally split the results into
per-chromosome vcfs.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
:param dict normal_bam: Dict o... | python | def run_somaticsniper(job, tumor_bam, normal_bam, univ_options, somaticsniper_options, split=True):
"""
Run the SomaticSniper subgraph on the DNA bams. Optionally split the results into
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BD2KGenomics/protect | src/protect/mutation_calling/somaticsniper.py | run_somaticsniper_full | def run_somaticsniper_full(job, tumor_bam, normal_bam, univ_options, somaticsniper_options):
"""
Run SomaticSniper on the DNA bams.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
:param dict normal_bam: Dict of bam and bai for normal DNA-Seq
:param dict univ_options: Dict of universal... | python | def run_somaticsniper_full(job, tumor_bam, normal_bam, univ_options, somaticsniper_options):
"""
Run SomaticSniper on the DNA bams.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
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BD2KGenomics/protect | src/protect/mutation_calling/somaticsniper.py | filter_somaticsniper | def filter_somaticsniper(job, tumor_bam, somaticsniper_output, tumor_pileup, univ_options,
somaticsniper_options):
"""
Filter SomaticSniper calls.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
:param toil.fileStore.FileID somaticsniper_output: SomaticSniper outpu... | python | def filter_somaticsniper(job, tumor_bam, somaticsniper_output, tumor_pileup, univ_options,
somaticsniper_options):
"""
Filter SomaticSniper calls.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
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BD2KGenomics/protect | src/protect/mutation_calling/somaticsniper.py | run_pileup | def run_pileup(job, tumor_bam, univ_options, somaticsniper_options):
"""
Runs a samtools pileup on the tumor bam.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
:param dict univ_options: Dict of universal options used by almost all tools
:param dict somaticsniper_options: Options spec... | python | def run_pileup(job, tumor_bam, univ_options, somaticsniper_options):
"""
Runs a samtools pileup on the tumor bam.
:param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
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