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broadinstitute/fiss | firecloud/fiss.py | attr_set | def attr_set(args):
''' Set key=value attributes: if entity name & type are specified then
attributes will be set upon that entity, otherwise the attribute will
be set at the workspace level'''
if args.entity_type and args.entity:
prompt = "Set {0}={1} for {2}:{3} in {4}/{5}?\n[Y\\n]: ".format(... | python | def attr_set(args):
''' Set key=value attributes: if entity name & type are specified then
attributes will be set upon that entity, otherwise the attribute will
be set at the workspace level'''
if args.entity_type and args.entity:
prompt = "Set {0}={1} for {2}:{3} in {4}/{5}?\n[Y\\n]: ".format(... | [
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broadinstitute/fiss | firecloud/fiss.py | attr_delete | def attr_delete(args):
''' Delete key=value attributes: if entity name & type are specified then
attributes will be deleted from that entity, otherwise the attribute will
be removed from the workspace'''
if args.entity_type and args.entities:
# Since there is no attribute deletion endpoint, we ... | python | def attr_delete(args):
''' Delete key=value attributes: if entity name & type are specified then
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broadinstitute/fiss | firecloud/fiss.py | attr_copy | def attr_copy(args):
""" Copy workspace attributes between workspaces. """
if not args.to_workspace:
args.to_workspace = args.workspace
if not args.to_project:
args.to_project = args.project
if (args.project == args.to_project
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epr... | python | def attr_copy(args):
""" Copy workspace attributes between workspaces. """
if not args.to_workspace:
args.to_workspace = args.workspace
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args.to_project = args.project
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broadinstitute/fiss | firecloud/fiss.py | attr_fill_null | def attr_fill_null(args):
"""
Assign the null sentinel value for all entities which do not have a value
for the given attributes.
see gs://broad-institute-gdac/GDAC_FC_NULL for more details
"""
NULL_SENTINEL = "gs://broad-institute-gdac/GDAC_FC_NULL"
attrs = args.attributes
if not attr... | python | def attr_fill_null(args):
"""
Assign the null sentinel value for all entities which do not have a value
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see gs://broad-institute-gdac/GDAC_FC_NULL for more details
"""
NULL_SENTINEL = "gs://broad-institute-gdac/GDAC_FC_NULL"
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broadinstitute/fiss | firecloud/fiss.py | health | def health(args):
""" Health FireCloud Server """
r = fapi.health()
fapi._check_response_code(r, 200)
return r.content | python | def health(args):
""" Health FireCloud Server """
r = fapi.health()
fapi._check_response_code(r, 200)
return r.content | [
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broadinstitute/fiss | firecloud/fiss.py | mop | def mop(args):
''' Clean up unreferenced data in a workspace'''
# First retrieve the workspace to get bucket information
if args.verbose:
print("Retrieving workspace information...")
r = fapi.get_workspace(args.project, args.workspace)
fapi._check_response_code(r, 200)
workspace = r.json... | python | def mop(args):
''' Clean up unreferenced data in a workspace'''
# First retrieve the workspace to get bucket information
if args.verbose:
print("Retrieving workspace information...")
r = fapi.get_workspace(args.project, args.workspace)
fapi._check_response_code(r, 200)
workspace = r.json... | [
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broadinstitute/fiss | firecloud/fiss.py | sset_loop | def sset_loop(args):
''' Loop over all sample sets in a workspace, performing a func '''
# Ensure that the requested action is a valid fiss_cmd
fiss_func = __cmd_to_func(args.action)
if not fiss_func:
eprint("invalid FISS cmd '" + args.action + "'")
return 1
# First get the sample s... | python | def sset_loop(args):
''' Loop over all sample sets in a workspace, performing a func '''
# Ensure that the requested action is a valid fiss_cmd
fiss_func = __cmd_to_func(args.action)
if not fiss_func:
eprint("invalid FISS cmd '" + args.action + "'")
return 1
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broadinstitute/fiss | firecloud/fiss.py | monitor | def monitor(args):
''' Retrieve status of jobs submitted from a given workspace, as a list
of TSV lines sorted by descending order of job submission date'''
r = fapi.list_submissions(args.project, args.workspace)
fapi._check_response_code(r, 200)
statuses = sorted(r.json(), key=lambda k: k['subm... | python | def monitor(args):
''' Retrieve status of jobs submitted from a given workspace, as a list
of TSV lines sorted by descending order of job submission date'''
r = fapi.list_submissions(args.project, args.workspace)
fapi._check_response_code(r, 200)
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broadinstitute/fiss | firecloud/fiss.py | supervise | def supervise(args):
''' Run legacy, Firehose-style workflow of workflows'''
project = args.project
workspace = args.workspace
namespace = args.namespace
workflow = args.workflow
sample_sets = args.sample_sets
recovery_file = args.json_checkpoint
# If no sample sets are provided, run on... | python | def supervise(args):
''' Run legacy, Firehose-style workflow of workflows'''
project = args.project
workspace = args.workspace
namespace = args.namespace
workflow = args.workflow
sample_sets = args.sample_sets
recovery_file = args.json_checkpoint
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broadinstitute/fiss | firecloud/fiss.py | entity_copy | def entity_copy(args):
""" Copy entities from one workspace to another. """
if not args.to_workspace:
args.to_workspace = args.workspace
if not args.to_project:
args.to_project = args.project
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""" Copy entities from one workspace to another. """
if not args.to_workspace:
args.to_workspace = args.workspace
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args.to_project = args.project
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broadinstitute/fiss | firecloud/fiss.py | proj_list | def proj_list(args):
'''Retrieve the list of billing projects accessible to the caller/user, and
show the level of access granted for each (e.g. Owner, User, ...)'''
projects = fapi.list_billing_projects()
fapi._check_response_code(projects, 200)
projects = sorted(projects.json(), key=lambda d: d... | python | def proj_list(args):
'''Retrieve the list of billing projects accessible to the caller/user, and
show the level of access granted for each (e.g. Owner, User, ...)'''
projects = fapi.list_billing_projects()
fapi._check_response_code(projects, 200)
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broadinstitute/fiss | firecloud/fiss.py | config_validate | def config_validate(args):
''' Validate a workspace configuration: if an entity was specified (i.e.
upon which the configuration should operate), then also validate that
the entity has the necessary attributes'''
r = fapi.validate_config(args.project, args.workspace, args.namespace,
... | python | def config_validate(args):
''' Validate a workspace configuration: if an entity was specified (i.e.
upon which the configuration should operate), then also validate that
the entity has the necessary attributes'''
r = fapi.validate_config(args.project, args.workspace, args.namespace,
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broadinstitute/fiss | firecloud/fiss.py | _validate_helper | def _validate_helper(args, config_d, workspace_d, entity_d=None):
""" Return FISSFC validation information on config for a certain entity """
# 4 ways to have invalid config:
invalid_inputs = sorted(config_d["invalidInputs"])
invalid_outputs = sorted(config_d["invalidOutputs"])
# Also insert va... | python | def _validate_helper(args, config_d, workspace_d, entity_d=None):
""" Return FISSFC validation information on config for a certain entity """
# 4 ways to have invalid config:
invalid_inputs = sorted(config_d["invalidInputs"])
invalid_outputs = sorted(config_d["invalidOutputs"])
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broadinstitute/fiss | firecloud/fiss.py | runnable | def runnable(args):
""" Show me what can be run in a given workspace """
w = fapi.get_workspace(args.project, args.workspace)
fapi._check_response_code(w, 200)
workspace_d = w.json()
if args.config and args.namespace and not args.entity:
# See what entities I can run on with this config
... | python | def runnable(args):
""" Show me what can be run in a given workspace """
w = fapi.get_workspace(args.project, args.workspace)
fapi._check_response_code(w, 200)
workspace_d = w.json()
if args.config and args.namespace and not args.entity:
# See what entities I can run on with this config
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broadinstitute/fiss | firecloud/fiss.py | _confirm_prompt | def _confirm_prompt(message, prompt="\nAre you sure? [y/yes (default: no)]: ",
affirmations=("Y", "Yes", "yes", "y")):
"""
Display a message, then confirmation prompt, and return true
if the user responds with one of the affirmations.
"""
answer = input(message + prompt)
retu... | python | def _confirm_prompt(message, prompt="\nAre you sure? [y/yes (default: no)]: ",
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broadinstitute/fiss | firecloud/fiss.py | _nonempty_project | def _nonempty_project(string):
"""
Argparse validator for ensuring a workspace is provided
"""
value = str(string)
if len(value) == 0:
msg = "No project provided and no default project configured"
raise argparse.ArgumentTypeError(msg)
return value | python | def _nonempty_project(string):
"""
Argparse validator for ensuring a workspace is provided
"""
value = str(string)
if len(value) == 0:
msg = "No project provided and no default project configured"
raise argparse.ArgumentTypeError(msg)
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broadinstitute/fiss | firecloud/fiss.py | _entity_paginator | def _entity_paginator(namespace, workspace, etype, page_size=500,
filter_terms=None, sort_direction="asc"):
"""Pages through the get_entities_query endpoint to get all entities in
the workspace without crashing.
"""
page = 1
all_entities = []
# Make initial reques... | python | def _entity_paginator(namespace, workspace, etype, page_size=500,
filter_terms=None, sort_direction="asc"):
"""Pages through the get_entities_query endpoint to get all entities in
the workspace without crashing.
"""
page = 1
all_entities = []
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broadinstitute/fiss | firecloud/fiss.py | __cmd_to_func | def __cmd_to_func(cmd):
""" Returns the function object in this module matching cmd. """
fiss_module = sys.modules[__name__]
# Returns None if string is not a recognized FISS command
func = getattr(fiss_module, cmd, None)
if func and not hasattr(func, 'fiss_cmd'):
func = None
return func | python | def __cmd_to_func(cmd):
""" Returns the function object in this module matching cmd. """
fiss_module = sys.modules[__name__]
# Returns None if string is not a recognized FISS command
func = getattr(fiss_module, cmd, None)
if func and not hasattr(func, 'fiss_cmd'):
func = None
return func | [
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broadinstitute/fiss | firecloud/fiss.py | _valid_headerline | def _valid_headerline(l):
"""return true if the given string is a valid loadfile header"""
if not l:
return False
headers = l.split('\t')
first_col = headers[0]
tsplit = first_col.split(':')
if len(tsplit) != 2:
return False
if tsplit[0] in ('entity', 'update'):
re... | python | def _valid_headerline(l):
"""return true if the given string is a valid loadfile header"""
if not l:
return False
headers = l.split('\t')
first_col = headers[0]
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broadinstitute/fiss | firecloud/fiss.py | _batch_load | def _batch_load(project, workspace, headerline, entity_data, chunk_size=500):
""" Submit a large number of entity updates in batches of chunk_size """
if fcconfig.verbosity:
print("Batching " + str(len(entity_data)) + " updates to Firecloud...")
# Parse the entity type from the first cell, e.g. "... | python | def _batch_load(project, workspace, headerline, entity_data, chunk_size=500):
""" Submit a large number of entity updates in batches of chunk_size """
if fcconfig.verbosity:
print("Batching " + str(len(entity_data)) + " updates to Firecloud...")
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broadinstitute/fiss | firecloud/fiss.py | main_as_cli | def main_as_cli(argv=None):
'''Use this entry point to call HL fiss funcs as though from the UNIX CLI.
(see firecloud/tests/highlevel_tests.py:call_cli for usage examples)'''
try:
result = main(argv)
except Exception as e:
result = __pretty_print_fc_exception(e)
# FIXME: we should... | python | def main_as_cli(argv=None):
'''Use this entry point to call HL fiss funcs as though from the UNIX CLI.
(see firecloud/tests/highlevel_tests.py:call_cli for usage examples)'''
try:
result = main(argv)
except Exception as e:
result = __pretty_print_fc_exception(e)
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broadinstitute/fiss | firecloud/entity.py | Entity.create_payload | def create_payload(entities):
"""Create a tsv payload describing entities.
A TSV payload consists of 1 header row describing entity type
and attribute names. Each subsequent line is an entity_id followed
by attribute values separated by the tab "\\t" character. This
payload can ... | python | def create_payload(entities):
"""Create a tsv payload describing entities.
A TSV payload consists of 1 header row describing entity type
and attribute names. Each subsequent line is an entity_id followed
by attribute values separated by the tab "\\t" character. This
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broadinstitute/fiss | firecloud/entity.py | Entity.create_loadfile | def create_loadfile(entities, f):
"""Create payload and save to file."""
with open(f, 'w') as out:
out.write(Entity.create_payload(entities)) | python | def create_loadfile(entities, f):
"""Create payload and save to file."""
with open(f, 'w') as out:
out.write(Entity.create_payload(entities)) | [
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broadinstitute/fiss | setup.py | InstallCommand.needs_gcloud | def needs_gcloud(self):
"""Returns true if gcloud is unavailable and needed for
authentication."""
gcloud_default_path = ['google-cloud-sdk', 'bin']
if platform.system() != "Windows":
gcloud_default_path = os.path.join(os.path.expanduser('~'),
... | python | def needs_gcloud(self):
"""Returns true if gcloud is unavailable and needed for
authentication."""
gcloud_default_path = ['google-cloud-sdk', 'bin']
if platform.system() != "Windows":
gcloud_default_path = os.path.join(os.path.expanduser('~'),
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fhcrc/seqmagick | seqmagick/subcommands/mogrify.py | action | def action(arguments):
"""
Run mogrify. Most of the action is in convert, this just creates a temp
file for the output.
"""
for input_file in arguments.input_files:
logging.info(input_file)
# Generate a temporary file
with common.atomic_write(
input_file.name... | python | def action(arguments):
"""
Run mogrify. Most of the action is in convert, this just creates a temp
file for the output.
"""
for input_file in arguments.input_files:
logging.info(input_file)
# Generate a temporary file
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | all_unambiguous | def all_unambiguous(sequence_str):
"""
All unambiguous versions of sequence_str
"""
result = [[]]
for c in sequence_str:
result = [i + [a] for i in result for a in _AMBIGUOUS_MAP.get(c, c)]
return [''.join(i) for i in result] | python | def all_unambiguous(sequence_str):
"""
All unambiguous versions of sequence_str
"""
result = [[]]
for c in sequence_str:
result = [i + [a] for i in result for a in _AMBIGUOUS_MAP.get(c, c)]
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | build_parser | def build_parser(parser):
"""
Generate a subparser
"""
parser.add_argument(
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type=FileType('r'),
help="""Input fastq file. A fasta-format file may also be provided
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parser.add_argument(
'--input-qual',
... | python | def build_parser(parser):
"""
Generate a subparser
"""
parser.add_argument(
'sequence_file',
type=FileType('r'),
help="""Input fastq file. A fasta-format file may also be provided
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | moving_average | def moving_average(iterable, n):
"""
From Python collections module documentation
moving_average([40, 30, 50, 46, 39, 44]) --> 40.0 42.0 45.0 43.0
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for elem in it:
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"""
From Python collections module documentation
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"""
it = iter(iterable)
d = collections.deque(itertools.islice(it, n - 1))
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | parse_barcode_file | def parse_barcode_file(fp, primer=None, header=False):
"""
Load label, barcode, primer records from a CSV file.
Returns a map from barcode -> label
Any additional columns are ignored
"""
tr = trie.trie()
reader = csv.reader(fp)
if header:
# Skip header
next(reader)
... | python | def parse_barcode_file(fp, primer=None, header=False):
"""
Load label, barcode, primer records from a CSV file.
Returns a map from barcode -> label
Any additional columns are ignored
"""
tr = trie.trie()
reader = csv.reader(fp)
if header:
# Skip header
next(reader)
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | action | def action(arguments):
"""
Given parsed arguments, filter input files.
"""
if arguments.quality_window_mean_qual and not arguments.quality_window:
raise ValueError("--quality-window-mean-qual specified without "
"--quality-window")
if trie is None or triefind is Non... | python | def action(arguments):
"""
Given parsed arguments, filter input files.
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | RecordEventListener.iterable_hook | def iterable_hook(self, name, iterable):
"""
Fire an event named ``name`` with each item in iterable
"""
for record in iterable:
self(name, record)
yield record | python | def iterable_hook(self, name, iterable):
"""
Fire an event named ``name`` with each item in iterable
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | RecordReportHandler._found_barcode | def _found_barcode(self, record, sample, barcode=None):
"""Hook called when barcode is found"""
assert record.id == self.current_record['sequence_name']
self.current_record['sample'] = sample | python | def _found_barcode(self, record, sample, barcode=None):
"""Hook called when barcode is found"""
assert record.id == self.current_record['sequence_name']
self.current_record['sample'] = sample | [
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | BaseFilter.filter_records | def filter_records(self, records):
"""
Apply the filter to records
"""
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# Quick tracking whether the sequence was modified
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | QualityScoreFilter.filter_record | def filter_record(self, record):
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Filter a single record
"""
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mean_score = mean(quality_scores)
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"""
Filter a single record
"""
quality_scores = record.letter_annotations['phred_quality']
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | WindowQualityScoreFilter.filter_record | def filter_record(self, record):
"""
Filter a single record
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if len(record) <= self.window_size:
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"""
Filter a single record
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | AmbiguousBaseFilter.filter_record | def filter_record(self, record):
"""
Filter a record, truncating or dropping at an 'N'
"""
nloc = record.seq.find('N')
if nloc == -1:
return record
elif self.action == 'truncate':
return record[:nloc]
elif self.action == 'drop':
... | python | def filter_record(self, record):
"""
Filter a record, truncating or dropping at an 'N'
"""
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | MinLengthFilter.filter_record | def filter_record(self, record):
"""
Filter record, dropping any that don't meet minimum length
"""
if len(record) >= self.min_length:
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Filter record, dropping any that don't meet minimum length
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | MaxLengthFilter.filter_record | def filter_record(self, record):
"""
Filter record, truncating any over some maximum length
"""
if len(record) >= self.max_length:
return record[:self.max_length]
else:
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Filter record, truncating any over some maximum length
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fhcrc/seqmagick | seqmagick/subcommands/info.py | summarize_sequence_file | def summarize_sequence_file(source_file, file_type=None):
"""
Summarizes a sequence file, returning a tuple containing the name,
whether the file is an alignment, minimum sequence length, maximum
sequence length, average length, number of sequences.
"""
is_alignment = True
avg_length = None
... | python | def summarize_sequence_file(source_file, file_type=None):
"""
Summarizes a sequence file, returning a tuple containing the name,
whether the file is an alignment, minimum sequence length, maximum
sequence length, average length, number of sequences.
"""
is_alignment = True
avg_length = None
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"""
Given one more more sequence files, determine if the file is an alignment,
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"""
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Given one more more sequence files, determine if the file is an alignment,
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fhcrc/seqmagick | seqmagick/transform.py | _record_buffer | def _record_buffer(records, buffer_size=DEFAULT_BUFFER_SIZE):
"""
Buffer for transform functions which require multiple passes through data.
Value returned by context manager is a function which returns an iterator
through records.
"""
with tempfile.SpooledTemporaryFile(buffer_size, mode='wb+')... | python | def _record_buffer(records, buffer_size=DEFAULT_BUFFER_SIZE):
"""
Buffer for transform functions which require multiple passes through data.
Value returned by context manager is a function which returns an iterator
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"""
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fhcrc/seqmagick | seqmagick/transform.py | dashes_cleanup | def dashes_cleanup(records, prune_chars='.:?~'):
"""
Take an alignment and convert any undesirable characters such as ? or ~ to
-.
"""
logging.info(
"Applying _dashes_cleanup: converting any of '{}' to '-'.".format(prune_chars))
translation_table = {ord(c): '-' for c in prune_chars}
... | python | def dashes_cleanup(records, prune_chars='.:?~'):
"""
Take an alignment and convert any undesirable characters such as ? or ~ to
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"""
logging.info(
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fhcrc/seqmagick | seqmagick/transform.py | deduplicate_sequences | def deduplicate_sequences(records, out_file):
"""
Remove any duplicate records with identical sequences, keep the first
instance seen and discard additional occurences.
"""
logging.info('Applying _deduplicate_sequences generator: '
'removing any duplicate records with identical seq... | python | def deduplicate_sequences(records, out_file):
"""
Remove any duplicate records with identical sequences, keep the first
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fhcrc/seqmagick | seqmagick/transform.py | deduplicate_taxa | def deduplicate_taxa(records):
"""
Remove any duplicate records with identical IDs, keep the first
instance seen and discard additional occurences.
"""
logging.info('Applying _deduplicate_taxa generator: ' + \
'removing any duplicate records with identical IDs.')
taxa = set()
... | python | def deduplicate_taxa(records):
"""
Remove any duplicate records with identical IDs, keep the first
instance seen and discard additional occurences.
"""
logging.info('Applying _deduplicate_taxa generator: ' + \
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taxa = set()
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fhcrc/seqmagick | seqmagick/transform.py | first_name_capture | def first_name_capture(records):
"""
Take only the first whitespace-delimited word as the name of the sequence.
Essentially removes any extra text from the sequence's description.
"""
logging.info('Applying _first_name_capture generator: '
'making sure ID only contains the first whi... | python | def first_name_capture(records):
"""
Take only the first whitespace-delimited word as the name of the sequence.
Essentially removes any extra text from the sequence's description.
"""
logging.info('Applying _first_name_capture generator: '
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fhcrc/seqmagick | seqmagick/transform.py | include_from_file | def include_from_file(records, handle):
"""
Filter the records, keeping only sequences whose ID is contained in the
handle.
"""
ids = set(i.strip() for i in handle)
for record in records:
if record.id.strip() in ids:
yield record | python | def include_from_file(records, handle):
"""
Filter the records, keeping only sequences whose ID is contained in the
handle.
"""
ids = set(i.strip() for i in handle)
for record in records:
if record.id.strip() in ids:
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fhcrc/seqmagick | seqmagick/transform.py | isolate_region | def isolate_region(sequences, start, end, gap_char='-'):
"""
Replace regions before and after start:end with gap chars
"""
# Check arguments
if end <= start:
raise ValueError("start of slice must precede end ({0} !> {1})".format(
end, start))
for sequence in sequences:
... | python | def isolate_region(sequences, start, end, gap_char='-'):
"""
Replace regions before and after start:end with gap chars
"""
# Check arguments
if end <= start:
raise ValueError("start of slice must precede end ({0} !> {1})".format(
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fhcrc/seqmagick | seqmagick/transform.py | drop_columns | def drop_columns(records, slices):
"""
Drop all columns present in ``slices`` from records
"""
for record in records:
# Generate a set of indices to remove
drop = set(i for slice in slices
for i in range(*slice.indices(len(record))))
keep = [i not in drop for i... | python | def drop_columns(records, slices):
"""
Drop all columns present in ``slices`` from records
"""
for record in records:
# Generate a set of indices to remove
drop = set(i for slice in slices
for i in range(*slice.indices(len(record))))
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fhcrc/seqmagick | seqmagick/transform.py | cut_sequences_relative | def cut_sequences_relative(records, slices, record_id):
"""
Cuts records to slices, indexed by non-gap positions in record_id
"""
with _record_buffer(records) as r:
try:
record = next(i for i in r() if i.id == record_id)
except StopIteration:
raise ValueError("Rec... | python | def cut_sequences_relative(records, slices, record_id):
"""
Cuts records to slices, indexed by non-gap positions in record_id
"""
with _record_buffer(records) as r:
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fhcrc/seqmagick | seqmagick/transform.py | multi_mask_sequences | def multi_mask_sequences(records, slices):
"""
Replace characters sliced by slices with gap characters.
"""
for record in records:
record_indices = list(range(len(record)))
keep_indices = reduce(lambda i, s: i - frozenset(record_indices[s]),
slices, frozense... | python | def multi_mask_sequences(records, slices):
"""
Replace characters sliced by slices with gap characters.
"""
for record in records:
record_indices = list(range(len(record)))
keep_indices = reduce(lambda i, s: i - frozenset(record_indices[s]),
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fhcrc/seqmagick | seqmagick/transform.py | prune_empty | def prune_empty(records):
"""
Remove any sequences which are entirely gaps ('-')
"""
for record in records:
if not all(c == '-' for c in str(record.seq)):
yield record | python | def prune_empty(records):
"""
Remove any sequences which are entirely gaps ('-')
"""
for record in records:
if not all(c == '-' for c in str(record.seq)):
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fhcrc/seqmagick | seqmagick/transform.py | _reverse_annotations | def _reverse_annotations(old_record, new_record):
"""
Copy annotations form old_record to new_record, reversing any
lists / tuples / strings.
"""
# Copy the annotations over
for k, v in list(old_record.annotations.items()):
# Trim if appropriate
if isinstance(v, (tuple, list)) an... | python | def _reverse_annotations(old_record, new_record):
"""
Copy annotations form old_record to new_record, reversing any
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"""
# Copy the annotations over
for k, v in list(old_record.annotations.items()):
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fhcrc/seqmagick | seqmagick/transform.py | reverse_sequences | def reverse_sequences(records):
"""
Reverse the order of sites in sequences.
"""
logging.info('Applying _reverse_sequences generator: '
'reversing the order of sites in sequences.')
for record in records:
rev_record = SeqRecord(record.seq[::-1], id=record.id,
... | python | def reverse_sequences(records):
"""
Reverse the order of sites in sequences.
"""
logging.info('Applying _reverse_sequences generator: '
'reversing the order of sites in sequences.')
for record in records:
rev_record = SeqRecord(record.seq[::-1], id=record.id,
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fhcrc/seqmagick | seqmagick/transform.py | reverse_complement_sequences | def reverse_complement_sequences(records):
"""
Transform sequences into reverse complements.
"""
logging.info('Applying _reverse_complement_sequences generator: '
'transforming sequences into reverse complements.')
for record in records:
rev_record = SeqRecord(record.seq.rev... | python | def reverse_complement_sequences(records):
"""
Transform sequences into reverse complements.
"""
logging.info('Applying _reverse_complement_sequences generator: '
'transforming sequences into reverse complements.')
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rev_record = SeqRecord(record.seq.rev... | [
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fhcrc/seqmagick | seqmagick/transform.py | ungap_sequences | def ungap_sequences(records, gap_chars=GAP_TABLE):
"""
Remove gaps from sequences, given an alignment.
"""
logging.info('Applying _ungap_sequences generator: removing all gap characters')
for record in records:
yield ungap_all(record, gap_chars) | python | def ungap_sequences(records, gap_chars=GAP_TABLE):
"""
Remove gaps from sequences, given an alignment.
"""
logging.info('Applying _ungap_sequences generator: removing all gap characters')
for record in records:
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fhcrc/seqmagick | seqmagick/transform.py | _update_id | def _update_id(record, new_id):
"""
Update a record id to new_id, also modifying the ID in record.description
"""
old_id = record.id
record.id = new_id
# At least for FASTA, record ID starts the description
record.description = re.sub('^' + re.escape(old_id), new_id, record.description)
... | python | def _update_id(record, new_id):
"""
Update a record id to new_id, also modifying the ID in record.description
"""
old_id = record.id
record.id = new_id
# At least for FASTA, record ID starts the description
record.description = re.sub('^' + re.escape(old_id), new_id, record.description)
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fhcrc/seqmagick | seqmagick/transform.py | name_append_suffix | def name_append_suffix(records, suffix):
"""
Given a set of sequences, append a suffix for each sequence's name.
"""
logging.info('Applying _name_append_suffix generator: '
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for record in records:
new... | python | def name_append_suffix(records, suffix):
"""
Given a set of sequences, append a suffix for each sequence's name.
"""
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fhcrc/seqmagick | seqmagick/transform.py | name_insert_prefix | def name_insert_prefix(records, prefix):
"""
Given a set of sequences, insert a prefix for each sequence's name.
"""
logging.info('Applying _name_insert_prefix generator: '
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for record in records:
ne... | python | def name_insert_prefix(records, prefix):
"""
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logging.info('Applying _name_insert_prefix generator: '
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fhcrc/seqmagick | seqmagick/transform.py | name_include | def name_include(records, filter_regex):
"""
Given a set of sequences, filter out any sequences with names
that do not match the specified regular expression. Ignore case.
"""
logging.info('Applying _name_include generator: '
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... | python | def name_include(records, filter_regex):
"""
Given a set of sequences, filter out any sequences with names
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fhcrc/seqmagick | seqmagick/transform.py | name_replace | def name_replace(records, search_regex, replace_pattern):
"""
Given a set of sequences, replace all occurrences of search_regex
with replace_pattern. Ignore case.
If the ID and the first word of the description match, assume the
description is FASTA-like and apply the transform to the entire
de... | python | def name_replace(records, search_regex, replace_pattern):
"""
Given a set of sequences, replace all occurrences of search_regex
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fhcrc/seqmagick | seqmagick/transform.py | seq_include | def seq_include(records, filter_regex):
"""
Filter any sequences who's seq does not match the filter. Ignore case.
"""
regex = re.compile(filter_regex)
for record in records:
if regex.search(str(record.seq)):
yield record | python | def seq_include(records, filter_regex):
"""
Filter any sequences who's seq does not match the filter. Ignore case.
"""
regex = re.compile(filter_regex)
for record in records:
if regex.search(str(record.seq)):
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fhcrc/seqmagick | seqmagick/transform.py | sample | def sample(records, k, random_seed=None):
"""Choose a length-``k`` subset of ``records``, retaining the input
order. If k > len(records), all are returned. If an integer
``random_seed`` is provided, sets ``random.seed()``
"""
if random_seed is not None:
random.seed(random_seed)
resul... | python | def sample(records, k, random_seed=None):
"""Choose a length-``k`` subset of ``records``, retaining the input
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``random_seed`` is provided, sets ``random.seed()``
"""
if random_seed is not None:
random.seed(random_seed)
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fhcrc/seqmagick | seqmagick/transform.py | head | def head(records, head):
"""
Limit results to the top N records.
With the leading `-', print all but the last N records.
"""
logging.info('Applying _head generator: '
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if head == '-0':
for record in records:
yi... | python | def head(records, head):
"""
Limit results to the top N records.
With the leading `-', print all but the last N records.
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logging.info('Applying _head generator: '
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fhcrc/seqmagick | seqmagick/transform.py | tail | def tail(records, tail):
"""
Limit results to the bottom N records.
Use +N to output records starting with the Nth.
"""
logging.info('Applying _tail generator: '
'limiting results to top ' + tail + ' records.')
if tail == '+0':
for record in records:
yield r... | python | def tail(records, tail):
"""
Limit results to the bottom N records.
Use +N to output records starting with the Nth.
"""
logging.info('Applying _tail generator: '
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fhcrc/seqmagick | seqmagick/transform.py | gap_proportion | def gap_proportion(sequences, gap_chars='-'):
"""
Generates a list with the proportion of gaps by index in a set of
sequences.
"""
aln_len = None
gaps = []
for i, sequence in enumerate(sequences):
if aln_len is None:
aln_len = len(sequence)
gaps = [0] * aln_le... | python | def gap_proportion(sequences, gap_chars='-'):
"""
Generates a list with the proportion of gaps by index in a set of
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"""
aln_len = None
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fhcrc/seqmagick | seqmagick/transform.py | squeeze | def squeeze(records, gap_threshold=1.0):
"""
Remove any gaps that are present in the same position across all sequences
in an alignment. Takes a second sequence iterator for determining gap
positions.
"""
with _record_buffer(records) as r:
gap_proportions = gap_proportion(r())
... | python | def squeeze(records, gap_threshold=1.0):
"""
Remove any gaps that are present in the same position across all sequences
in an alignment. Takes a second sequence iterator for determining gap
positions.
"""
with _record_buffer(records) as r:
gap_proportions = gap_proportion(r())
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"""
logging.info('Applying _strip_range generator: '
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"""
Cut off trailing /<start>-<stop> ranges from IDs. Ranges must be 1-indexed and
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"""
logging.info('Applying _strip_range generator: '
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fhcrc/seqmagick | seqmagick/transform.py | transcribe | def transcribe(records, transcribe):
"""
Perform transcription or back-transcription.
transcribe must be one of the following:
dna2rna
rna2dna
"""
logging.info('Applying _transcribe generator: '
'operation to perform is ' + transcribe + '.')
for record in records... | python | def transcribe(records, transcribe):
"""
Perform transcription or back-transcription.
transcribe must be one of the following:
dna2rna
rna2dna
"""
logging.info('Applying _transcribe generator: '
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fhcrc/seqmagick | seqmagick/transform.py | translate | def translate(records, translate):
"""
Perform translation from generic DNA/RNA to proteins. Bio.Seq
does not perform back-translation because the codons would
more-or-less be arbitrary. Option to translate only up until
reaching a stop codon. translate must be one of the following:
dna2p... | python | def translate(records, translate):
"""
Perform translation from generic DNA/RNA to proteins. Bio.Seq
does not perform back-translation because the codons would
more-or-less be arbitrary. Option to translate only up until
reaching a stop codon. translate must be one of the following:
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fhcrc/seqmagick | seqmagick/transform.py | max_length_discard | def max_length_discard(records, max_length):
"""
Discard any records that are longer than max_length.
"""
logging.info('Applying _max_length_discard generator: '
'discarding records longer than '
'.')
for record in records:
if len(record) > max_length:
... | python | def max_length_discard(records, max_length):
"""
Discard any records that are longer than max_length.
"""
logging.info('Applying _max_length_discard generator: '
'discarding records longer than '
'.')
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if len(record) > max_length:
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fhcrc/seqmagick | seqmagick/transform.py | min_length_discard | def min_length_discard(records, min_length):
"""
Discard any records that are shorter than min_length.
"""
logging.info('Applying _min_length_discard generator: '
'discarding records shorter than %d.', min_length)
for record in records:
if len(record) < min_length:
... | python | def min_length_discard(records, min_length):
"""
Discard any records that are shorter than min_length.
"""
logging.info('Applying _min_length_discard generator: '
'discarding records shorter than %d.', min_length)
for record in records:
if len(record) < min_length:
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fhcrc/seqmagick | seqmagick/transform.py | min_ungap_length_discard | def min_ungap_length_discard(records, min_length):
"""
Discard any records that are shorter than min_length after removing gaps.
"""
for record in records:
if len(ungap_all(record)) >= min_length:
yield record | python | def min_ungap_length_discard(records, min_length):
"""
Discard any records that are shorter than min_length after removing gaps.
"""
for record in records:
if len(ungap_all(record)) >= min_length:
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fhcrc/seqmagick | seqmagick/transform.py | sort_length | def sort_length(source_file, source_file_type, direction=1):
"""
Sort sequences by length. 1 is ascending (default) and 0 is descending.
"""
direction_text = 'ascending' if direction == 1 else 'descending'
logging.info('Indexing sequences by length: %s', direction_text)
# Adapted from the Biop... | python | def sort_length(source_file, source_file_type, direction=1):
"""
Sort sequences by length. 1 is ascending (default) and 0 is descending.
"""
direction_text = 'ascending' if direction == 1 else 'descending'
logging.info('Indexing sequences by length: %s', direction_text)
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fhcrc/seqmagick | seqmagick/subcommands/backtrans_align.py | batch | def batch(iterable, chunk_size):
"""
Return items from iterable in chunk_size bits.
If len(iterable) % chunk_size > 0, the last item returned will be shorter.
"""
i = iter(iterable)
while True:
r = list(itertools.islice(i, chunk_size))
if not r:
break
yield r | python | def batch(iterable, chunk_size):
"""
Return items from iterable in chunk_size bits.
If len(iterable) % chunk_size > 0, the last item returned will be shorter.
"""
i = iter(iterable)
while True:
r = list(itertools.islice(i, chunk_size))
if not r:
break
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fhcrc/seqmagick | seqmagick/subcommands/backtrans_align.py | action | def action(arguments):
"""
Run
"""
# Ignore SIGPIPE, for head support
common.exit_on_sigpipe()
logging.basicConfig()
prot_sequences = SeqIO.parse(arguments.protein_align,
fileformat.from_handle(arguments.protein_align))
nucl_sequences = SeqIO.parse(argum... | python | def action(arguments):
"""
Run
"""
# Ignore SIGPIPE, for head support
common.exit_on_sigpipe()
logging.basicConfig()
prot_sequences = SeqIO.parse(arguments.protein_align,
fileformat.from_handle(arguments.protein_align))
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fhcrc/seqmagick | seqmagick/subcommands/backtrans_align.py | AlignmentMapper._validate_translation | def _validate_translation(self, aligned_prot, aligned_nucl):
"""
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"""
codons = [''.join(i) for i in batch(str(aligned_nucl), 3)]
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# Check gaps
... | python | def _validate_translation(self, aligned_prot, aligned_nucl):
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fhcrc/seqmagick | seqmagick/subcommands/backtrans_align.py | AlignmentMapper.map_alignment | def map_alignment(self, prot_seq, nucl_seq):
"""
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logging.warning(
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# Unga... | python | def map_alignment(self, prot_seq, nucl_seq):
"""
Use aligned prot_seq to align nucl_seq
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if prot_seq.id != nucl_seq.id:
logging.warning(
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fhcrc/seqmagick | seqmagick/subcommands/backtrans_align.py | AlignmentMapper.map_all | def map_all(self, prot_alignment, nucl_sequences):
"""
Convert protein sequences to nucleotide alignment
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zipped = itertools.zip_longest(prot_alignment, nucl_sequences)
for p, n in zipped:
if p is None:
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fhcrc/seqmagick | seqmagick/fileformat.py | from_extension | def from_extension(extension):
"""
Look up the BioPython file type corresponding with input extension.
Look up is case insensitive.
"""
if not extension.startswith('.'):
raise ValueError("Extensions must begin with a period.")
try:
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"""
Look up the BioPython file type corresponding with input extension.
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fhcrc/seqmagick | seqmagick/fileformat.py | from_filename | def from_filename(file_name):
"""
Look up the BioPython file type corresponding to an input file name.
"""
base, extension = os.path.splitext(file_name)
if extension in COMPRESS_EXT:
# Compressed file
extension = os.path.splitext(base)[1]
return from_extension(extension) | python | def from_filename(file_name):
"""
Look up the BioPython file type corresponding to an input file name.
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base, extension = os.path.splitext(file_name)
if extension in COMPRESS_EXT:
# Compressed file
extension = os.path.splitext(base)[1]
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fhcrc/seqmagick | seqmagick/fileformat.py | from_handle | def from_handle(fh, stream_default='fasta'):
"""
Look up the BioPython file type corresponding to a file-like object.
For stdin, stdout, and stderr, ``stream_default`` is used.
"""
if fh in (sys.stdin, sys.stdout, sys.stderr):
return stream_default
return from_filename(fh.name) | python | def from_handle(fh, stream_default='fasta'):
"""
Look up the BioPython file type corresponding to a file-like object.
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if fh in (sys.stdin, sys.stdout, sys.stderr):
return stream_default
return from_filename(fh.name) | [
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fhcrc/seqmagick | seqmagick/scripts/cli.py | parse_arguments | def parse_arguments(argv):
"""
Extract command-line arguments for different actions.
"""
parser = argparse.ArgumentParser(description='seqmagick - Manipulate ' + \
' sequence files.', prog='seqmagick')
parser.add_argument('-V', '--version', action='version',
version='seqmagick v'... | python | def parse_arguments(argv):
"""
Extract command-line arguments for different actions.
"""
parser = argparse.ArgumentParser(description='seqmagick - Manipulate ' + \
' sequence files.', prog='seqmagick')
parser.add_argument('-V', '--version', action='version',
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | ungap_index_map | def ungap_index_map(sequence, gap_chars='-'):
"""
Returns a dict mapping from an index in the ungapped sequence to an index
in the gapped sequence.
>>> ungap_index_map('AC-TG-')
{0: 0, 1: 1, 2: 3, 3: 4}
"""
counter = itertools.count(0).__next__
ungap_indexes = [
counter() if c n... | python | def ungap_index_map(sequence, gap_chars='-'):
"""
Returns a dict mapping from an index in the ungapped sequence to an index
in the gapped sequence.
>>> ungap_index_map('AC-TG-')
{0: 0, 1: 1, 2: 3, 3: 4}
"""
counter = itertools.count(0).__next__
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | gap_index_map | def gap_index_map(sequence, gap_chars='-'):
"""
Opposite of ungap_index_map: returns mapping from gapped index to ungapped
index.
>>> gap_index_map('AC-TG-')
{0: 0, 1: 1, 3: 2, 4: 3}
"""
return dict(
(v, k) for k, v in list(ungap_index_map(sequence, gap_chars).items())) | python | def gap_index_map(sequence, gap_chars='-'):
"""
Opposite of ungap_index_map: returns mapping from gapped index to ungapped
index.
>>> gap_index_map('AC-TG-')
{0: 0, 1: 1, 3: 2, 4: 3}
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | _iupac_ambiguous_equal | def _iupac_ambiguous_equal(ambig_base, unambig_base):
"""
Tests two bases for equality, accounting for IUPAC ambiguous DNA
ambiguous base may be IUPAC ambiguous, unambiguous must be one of ACGT
"""
iupac_translation = {
'A': 'A',
'C': 'C',
'G': 'G',
'T': 'T',
... | python | def _iupac_ambiguous_equal(ambig_base, unambig_base):
"""
Tests two bases for equality, accounting for IUPAC ambiguous DNA
ambiguous base may be IUPAC ambiguous, unambiguous must be one of ACGT
"""
iupac_translation = {
'A': 'A',
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'G': 'G',
'T': 'T',
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | hamming_distance | def hamming_distance(s1, s2, equality_function=operator.eq):
"""
Returns the hamming distance between two strings.
"""
if not len(s1) == len(s2):
raise ValueError("String lengths are not equal")
# Number of non-matching characters:
return sum(not equality_function(c1, c2) for c1, c2 in ... | python | def hamming_distance(s1, s2, equality_function=operator.eq):
"""
Returns the hamming distance between two strings.
"""
if not len(s1) == len(s2):
raise ValueError("String lengths are not equal")
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | locate_primers | def locate_primers(sequences, forward_primer, reverse_primer,
reverse_complement, max_hamming_distance):
"""
Find forward and reverse primers in a set of sequences, return two tuples:
(forward_start, forward_end), (reverse_start, reverse_end)
"""
forward_loc = None
reverse_loc... | python | def locate_primers(sequences, forward_primer, reverse_primer,
reverse_complement, max_hamming_distance):
"""
Find forward and reverse primers in a set of sequences, return two tuples:
(forward_start, forward_end), (reverse_start, reverse_end)
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forward_loc = None
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | trim | def trim(sequences, start, end):
"""
Slice the input sequences from start to end
"""
logging.info("Trimming from %d to %d", start, end)
return (sequence[start:end] for sequence in sequences) | python | def trim(sequences, start, end):
"""
Slice the input sequences from start to end
"""
logging.info("Trimming from %d to %d", start, end)
return (sequence[start:end] for sequence in sequences) | [
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | action | def action(arguments):
"""
Trim the alignment as specified
"""
# Determine file format for input and output
source_format = (arguments.source_format or
fileformat.from_handle(arguments.source_file))
output_format = (arguments.output_format or
fileformat.... | python | def action(arguments):
"""
Trim the alignment as specified
"""
# Determine file format for input and output
source_format = (arguments.source_format or
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fhcrc/seqmagick | seqmagick/subcommands/primer_trim.py | PrimerAligner.align | def align(self, sequence):
"""
Aligns the primer to the given query sequence, returning a tuple of:
hamming_distance, start, end
Where hamming distance is the distance between the primer and aligned
sequence, and start and end give the start and end index of the primer
... | python | def align(self, sequence):
"""
Aligns the primer to the given query sequence, returning a tuple of:
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fhcrc/seqmagick | examples/apply-function/myfunctions.py | hash_starts_numeric | def hash_starts_numeric(records):
"""
Very useful function that only accepts records with a numeric start to
their sha-1 hash.
"""
for record in records:
seq_hash = hashlib.sha1(str(record.seq)).hexdigest()
if seq_hash[0].isdigit():
yield record | python | def hash_starts_numeric(records):
"""
Very useful function that only accepts records with a numeric start to
their sha-1 hash.
"""
for record in records:
seq_hash = hashlib.sha1(str(record.seq)).hexdigest()
if seq_hash[0].isdigit():
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fhcrc/seqmagick | seqmagick/subcommands/common.py | atomic_write | def atomic_write(path, mode='wt', permissions=None, file_factory=None, **kwargs):
"""
Open a file for atomic writing.
Generates a temp file, renames to value of ``path``.
Arguments:
``permissions``: Permissions to set (default: umask)
``file_factory``: If given, the handle yielded will be the ... | python | def atomic_write(path, mode='wt', permissions=None, file_factory=None, **kwargs):
"""
Open a file for atomic writing.
Generates a temp file, renames to value of ``path``.
Arguments:
``permissions``: Permissions to set (default: umask)
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fhcrc/seqmagick | seqmagick/subcommands/common.py | cut_range | def cut_range(string):
"""
A custom argparse 'type' to deal with sequences ranges such as 5:500.
Returns a 0-based slice corresponding to the selection defined by the slice
"""
value_range = string.split(':')
if len(value_range) == 1:
start = int(value_range[0])
stop = start
... | python | def cut_range(string):
"""
A custom argparse 'type' to deal with sequences ranges such as 5:500.
Returns a 0-based slice corresponding to the selection defined by the slice
"""
value_range = string.split(':')
if len(value_range) == 1:
start = int(value_range[0])
stop = start
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fhcrc/seqmagick | seqmagick/subcommands/common.py | typed_range | def typed_range(type_func, minimum, maximum):
"""
Require variables to be of the specified type, between minimum and maximum
"""
@functools.wraps(type_func)
def inner(string):
result = type_func(string)
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raise argparse.Argume... | python | def typed_range(type_func, minimum, maximum):
"""
Require variables to be of the specified type, between minimum and maximum
"""
@functools.wraps(type_func)
def inner(string):
result = type_func(string)
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fhcrc/seqmagick | seqmagick/subcommands/common.py | partial_append_action | def partial_append_action(fn, argument_keys=None):
"""
Creates a new class extending argparse.Action, which appends a
partially-applied function to dest.
The optional argument_keys argument should either be None (no additional
arguments to fn) or an iterable of function keys to partially apply.
... | python | def partial_append_action(fn, argument_keys=None):
"""
Creates a new class extending argparse.Action, which appends a
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The optional argument_keys argument should either be None (no additional
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fhcrc/seqmagick | seqmagick/subcommands/common.py | positive_value | def positive_value(target_type):
"""
Wraps target_type in a function that requires the parsed argument
be >= 0
"""
def inner(string):
value = target_type(string)
if not value >= 0:
raise argparse.ArgumentTypeError("Invalid positive number: " +
string)
... | python | def positive_value(target_type):
"""
Wraps target_type in a function that requires the parsed argument
be >= 0
"""
def inner(string):
value = target_type(string)
if not value >= 0:
raise argparse.ArgumentTypeError("Invalid positive number: " +
string)
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fhcrc/seqmagick | seqmagick/subcommands/convert.py | add_options | def add_options(parser):
"""
Add optional arguments to the parser
"""
partial_action = common.partial_append_action
file_mods = parser.add_argument_group("Sequence File Modification")
file_mods.add_argument('--line-wrap', dest='line_wrap', metavar='N',
type=int, help='Adjust line wrap fo... | python | def add_options(parser):
"""
Add optional arguments to the parser
"""
partial_action = common.partial_append_action
file_mods = parser.add_argument_group("Sequence File Modification")
file_mods.add_argument('--line-wrap', dest='line_wrap', metavar='N',
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fhcrc/seqmagick | seqmagick/subcommands/convert.py | build_parser | def build_parser(parser):
"""
Add shared arguments to the convert or mogrify parser.
"""
add_options(parser)
parser.add_argument('source_file', type=common.FileType('rt'),
help="Input sequence file")
parser.add_argument('dest_file', help="Output file")
return parser | python | def build_parser(parser):
"""
Add shared arguments to the convert or mogrify parser.
"""
add_options(parser)
parser.add_argument('source_file', type=common.FileType('rt'),
help="Input sequence file")
parser.add_argument('dest_file', help="Output file")
return parser | [
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fhcrc/seqmagick | seqmagick/subcommands/convert.py | module_function | def module_function(string):
"""
Load a function from a python module using a file name, function name
specification of format:
/path/to/x.py:function_name[:parameter]
"""
parts = string.split(':', 2)
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raise ValueError(
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"""
Load a function from a python module using a file name, function name
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/path/to/x.py:function_name[:parameter]
"""
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phac-nml/sistr_cmd | sistr/misc/reduce_to_centroid_alleles.py | parse_cgmlst_alleles | def parse_cgmlst_alleles(cgmlst_fasta):
"""Parse cgMLST alleles from fasta file
cgMLST FASTA file must have a header format of ">{marker name}|{allele name}"
Args:
cgmlst_fasta (str): cgMLST fasta file path
Returns:
dict of list: Marker name to list of allele sequences
"""
out ... | python | def parse_cgmlst_alleles(cgmlst_fasta):
"""Parse cgMLST alleles from fasta file
cgMLST FASTA file must have a header format of ">{marker name}|{allele name}"
Args:
cgmlst_fasta (str): cgMLST fasta file path
Returns:
dict of list: Marker name to list of allele sequences
"""
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cgmlst_fasta (str): cgMLST fasta file path
Returns:
dict of list: Marker name to list of allele sequences | [
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