sentence1 stringlengths 52 3.87M | sentence2 stringlengths 1 47.2k | label stringclasses 1
value |
|---|---|---|
def entity_delete(args):
""" Delete entity in a workspace. """
msg = "WARNING: this will delete {0} {1} in {2}/{3}".format(
args.entity_type, args.entity, args.project, args.workspace)
if not (args.yes or _confirm_prompt(msg)):
return
json_body=[{"entityType": args.entity_type,
... | Delete entity in a workspace. | entailment |
def meth_new(args):
""" Submit a new workflow (or update) to the methods repository. """
r = fapi.update_repository_method(args.namespace, args.method,
args.synopsis, args.wdl, args.doc,
args.comment)
fapi._check_response_code(r, 20... | Submit a new workflow (or update) to the methods repository. | entailment |
def meth_delete(args):
""" Remove (redact) a method from the method repository """
message = "WARNING: this will delete workflow \n\t{0}/{1}:{2}".format(
args.namespace, args.method, args.snapshot_id)
if not args.yes and not _confirm_prompt(message):
return
r... | Remove (redact) a method from the method repository | entailment |
def meth_wdl(args):
''' Retrieve WDL for given version of a repository method'''
r = fapi.get_repository_method(args.namespace, args.method,
args.snapshot_id, True)
fapi._check_response_code(r, 200)
return r.text | Retrieve WDL for given version of a repository method | entailment |
def meth_acl(args):
''' Retrieve access control list for given version of a repository method'''
r = fapi.get_repository_method_acl(args.namespace, args.method,
args.snapshot_id)
fapi._check_response_code(r, 200)
acls = sorted(r.json(), key=lambda k: k... | Retrieve access control list for given version of a repository method | entailment |
def meth_set_acl(args):
""" Assign an ACL role to a list of users for a workflow. """
acl_updates = [{"user": user, "role": args.role} \
for user in set(expand_fc_groups(args.users)) \
if user != fapi.whoami()]
id = args.snapshot_id
if not id:
# get the lat... | Assign an ACL role to a list of users for a workflow. | entailment |
def expand_fc_groups(users):
""" If user is a firecloud group, return all members of the group.
Caveat is that only group admins may do this.
"""
groups = None
for user in users:
fcgroup = None
if '@' not in user:
fcgroup = user
elif user.lower().endswith('@firecl... | If user is a firecloud group, return all members of the group.
Caveat is that only group admins may do this. | entailment |
def meth_list(args):
""" List workflows in the methods repository """
r = fapi.list_repository_methods(namespace=args.namespace,
name=args.method,
snapshotId=args.snapshot_id)
fapi._check_response_code(r, 200)
# Parse the JSON fo... | List workflows in the methods repository | entailment |
def config_start(args):
'''Invoke a task (method configuration), on given entity in given space'''
# Try to use call caching (job avoidance)? Flexibly accept range of answers
cache = getattr(args, "cache", True)
cache = cache is True or (cache.lower() in ["y", "true", "yes", "t", "1"])
if not arg... | Invoke a task (method configuration), on given entity in given space | entailment |
def config_stop(args):
'''Abort a task (method configuration) by submission ID in given space'''
r = fapi.abort_submission(args.project, args.workspace,
args.submission_id)
fapi._check_response_code(r, 204)
return ("Aborted {0} in {1}/{2}".format(args.submission_id,
... | Abort a task (method configuration) by submission ID in given space | entailment |
def config_list(args):
""" List configuration(s) in the methods repository or a workspace. """
verbose = fcconfig.verbosity
if args.workspace:
if verbose:
print("Retrieving method configs from space {0}".format(args.workspace))
if not args.project:
eprint("No project ... | List configuration(s) in the methods repository or a workspace. | entailment |
def config_acl(args):
''' Retrieve access control list for a method configuration'''
r = fapi.get_repository_config_acl(args.namespace, args.config,
args.snapshot_id)
fapi._check_response_code(r, 200)
acls = sorted(r.json(), key=lambda k: k['user'])
... | Retrieve access control list for a method configuration | entailment |
def config_set_acl(args):
""" Assign an ACL role to a list of users for a config. """
acl_updates = [{"user": user, "role": args.role} \
for user in set(expand_fc_groups(args.users)) \
if user != fapi.whoami()]
id = args.snapshot_id
if not id:
# get the lat... | Assign an ACL role to a list of users for a config. | entailment |
def config_get(args):
""" Retrieve a method config from a workspace, send stdout """
r = fapi.get_workspace_config(args.project, args.workspace,
args.namespace, args.config)
fapi._check_response_code(r, 200)
# Setting ensure_ascii to False ensures unicode string r... | Retrieve a method config from a workspace, send stdout | entailment |
def config_wdl(args):
""" Retrieve the WDL for a method config in a workspace, send stdout """
r = fapi.get_workspace_config(args.project, args.workspace,
args.namespace, args.config)
fapi._check_response_code(r, 200)
method = r.json()["methodRepoMethod"]
args.... | Retrieve the WDL for a method config in a workspace, send stdout | entailment |
def config_diff(args):
"""Compare method configuration definitions across workspaces. Ignores
methodConfigVersion if the verbose argument is not set"""
config_1 = config_get(args).splitlines()
args.project = args.Project
args.workspace = args.Workspace
cfg_1_name = args.config
if args.Con... | Compare method configuration definitions across workspaces. Ignores
methodConfigVersion if the verbose argument is not set | entailment |
def config_put(args):
'''Install a valid method configuration into a workspace, in one of several
ways: from a JSON file containing a config definition (both file names
and objects are supported); as a string representing the content of such
a JSON file; or as a dict generated from such JSON co... | Install a valid method configuration into a workspace, in one of several
ways: from a JSON file containing a config definition (both file names
and objects are supported); as a string representing the content of such
a JSON file; or as a dict generated from such JSON content, e.g via
json.lo... | entailment |
def config_new(args):
'''Attempt to install a new method config into a workspace, by: generating
a template from a versioned method in the methods repo, then launching
a local editor (respecting the $EDITOR environment variable) to fill in
the incomplete input/output fields. Returns True if th... | Attempt to install a new method config into a workspace, by: generating
a template from a versioned method in the methods repo, then launching
a local editor (respecting the $EDITOR environment variable) to fill in
the incomplete input/output fields. Returns True if the config was
successfu... | entailment |
def config_delete(args):
""" Remove a method config from a workspace """
r = fapi.delete_workspace_config(args.project, args.workspace,
args.namespace, args.config)
fapi._check_response_code(r, [200,204])
return r.text if r.text else None | Remove a method config from a workspace | entailment |
def config_copy(args):
""" Copy a method config to new name/space/namespace/project (or all 4) """
if not (args.tospace or args.toname or args.toproject or args.tonamespace):
raise RuntimeError('A new config name OR workspace OR project OR ' +
'namespace must be given (or all)... | Copy a method config to new name/space/namespace/project (or all 4) | entailment |
def attr_get(args):
'''Return a dict of attribute name/value pairs: if entity name & type
are specified then attributes will be retrieved from that entity,
otherwise workspace-level attributes will be returned. By default all
attributes attached to the given object will be returned, but a subset
ca... | Return a dict of attribute name/value pairs: if entity name & type
are specified then attributes will be retrieved from that entity,
otherwise workspace-level attributes will be returned. By default all
attributes attached to the given object will be returned, but a subset
can be selected by specifying... | entailment |
def attr_list(args):
'''Retrieve names of all attributes attached to a given object, either
an entity (if entity type+name is provided) or workspace (if not)'''
args.attributes = None
result = attr_get(args)
names = result.get("__header__",[])
if names:
names = names[1:]
else:
... | Retrieve names of all attributes attached to a given object, either
an entity (if entity type+name is provided) or workspace (if not) | entailment |
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(... | 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 | entailment |
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 ... | 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 | entailment |
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
and args.workspace == args.to_workspace):
epr... | Copy workspace attributes between workspaces. | entailment |
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... | 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 | entailment |
def health(args):
""" Health FireCloud Server """
r = fapi.health()
fapi._check_response_code(r, 200)
return r.content | Health FireCloud Server | entailment |
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... | Clean up unreferenced data in a workspace | entailment |
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... | Loop over all sample sets in a workspace, performing a func | entailment |
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... | Retrieve status of jobs submitted from a given workspace, as a list
of TSV lines sorted by descending order of job submission date | entailment |
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... | Run legacy, Firehose-style workflow of workflows | entailment |
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
if (args.project == args.to_project
and args.workspace == args.to_workspace):
ep... | Copy entities from one workspace to another. | entailment |
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... | Retrieve the list of billing projects accessible to the caller/user, and
show the level of access granted for each (e.g. Owner, User, ...) | entailment |
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,
... | 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 | entailment |
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... | Return FISSFC validation information on config for a certain entity | entailment |
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
... | Show me what can be run in a given workspace | entailment |
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... | Display a message, then confirmation prompt, and return true
if the user responds with one of the affirmations. | entailment |
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 | Argparse validator for ensuring a workspace is provided | entailment |
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... | Pages through the get_entities_query endpoint to get all entities in
the workspace without crashing. | entailment |
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 | Returns the function object in this module matching cmd. | entailment |
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... | return true if the given string is a valid loadfile header | entailment |
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. "... | Submit a large number of entity updates in batches of chunk_size | entailment |
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... | 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) | entailment |
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 ... | 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 be uploaded to the workspace via
... | entailment |
def create_loadfile(entities, f):
"""Create payload and save to file."""
with open(f, 'w') as out:
out.write(Entity.create_payload(entities)) | Create payload and save to file. | entailment |
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('~'),
... | Returns true if gcloud is unavailable and needed for
authentication. | entailment |
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... | Run mogrify. Most of the action is in convert, this just creates a temp
file for the output. | entailment |
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] | All unambiguous versions of sequence_str | entailment |
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
if --input-qual is also specified.""")
parser.add_argument(
'--input-qual',
... | Generate a subparser | entailment |
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
"""
it = iter(iterable)
d = collections.deque(itertools.islice(it, n - 1))
d.appendleft(0)
s = sum(d)
for elem in it:
s += elem ... | From Python collections module documentation
moving_average([40, 30, 50, 46, 39, 44]) --> 40.0 42.0 45.0 43.0 | entailment |
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)
... | Load label, barcode, primer records from a CSV file.
Returns a map from barcode -> label
Any additional columns are ignored | entailment |
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... | Given parsed arguments, filter input files. | entailment |
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 | Fire an event named ``name`` with each item in iterable | entailment |
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 | Hook called when barcode is found | entailment |
def filter_records(self, records):
"""
Apply the filter to records
"""
for record in records:
try:
filtered = self.filter_record(record)
assert (filtered)
# Quick tracking whether the sequence was modified
if fil... | Apply the filter to records | entailment |
def filter_record(self, record):
"""
Filter a single record
"""
quality_scores = record.letter_annotations['phred_quality']
mean_score = mean(quality_scores)
if mean_score >= self.min_mean_score:
return record
else:
raise FailedFilter(mean... | Filter a single record | entailment |
def filter_record(self, record):
"""
Filter a single record
"""
quality_scores = record.letter_annotations['phred_quality']
# Simple case - window covers whole sequence
if len(record) <= self.window_size:
mean_score = mean(quality_scores)
if mean_... | Filter a single record | entailment |
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':
... | Filter a record, truncating or dropping at an 'N' | entailment |
def filter_record(self, record):
"""
Filter record, dropping any that don't meet minimum length
"""
if len(record) >= self.min_length:
return record
else:
raise FailedFilter(len(record)) | Filter record, dropping any that don't meet minimum length | entailment |
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:
return record | Filter record, truncating any over some maximum length | entailment |
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
... | 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. | entailment |
def action(arguments):
"""
Given one more more sequence files, determine if the file is an alignment,
the maximum sequence length and the total number of sequences. Provides
different output formats including tab (tab-delimited), csv and align
(aligned as if part of a borderless table).
"""
... | Given one more more sequence files, determine if the file is an alignment,
the maximum sequence length and the total number of sequences. Provides
different output formats including tab (tab-delimited), csv and align
(aligned as if part of a borderless table). | entailment |
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+')... | Buffer for transform functions which require multiple passes through data.
Value returned by context manager is a function which returns an iterator
through records. | entailment |
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}
... | Take an alignment and convert any undesirable characters such as ? or ~ to
-. | entailment |
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... | Remove any duplicate records with identical sequences, keep the first
instance seen and discard additional occurences. | entailment |
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()
... | Remove any duplicate records with identical IDs, keep the first
instance seen and discard additional occurences. | entailment |
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... | Take only the first whitespace-delimited word as the name of the sequence.
Essentially removes any extra text from the sequence's description. | entailment |
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 | Filter the records, keeping only sequences whose ID is contained in the
handle. | entailment |
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:
... | Replace regions before and after start:end with gap chars | entailment |
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... | Drop all columns present in ``slices`` from records | entailment |
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... | Cuts records to slices, indexed by non-gap positions in record_id | entailment |
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... | Replace characters sliced by slices with gap characters. | entailment |
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 | Remove any sequences which are entirely gaps ('-') | entailment |
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... | Copy annotations form old_record to new_record, reversing any
lists / tuples / strings. | entailment |
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,
... | Reverse the order of sites in sequences. | entailment |
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... | Transform sequences into reverse complements. | entailment |
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) | Remove gaps from sequences, given an alignment. | entailment |
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)
... | Update a record id to new_id, also modifying the ID in record.description | entailment |
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: '
'Appending suffix ' + suffix + ' to all '
'sequence IDs.')
for record in records:
new... | Given a set of sequences, append a suffix for each sequence's name. | entailment |
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: '
'Inserting prefix ' + prefix + ' for all '
'sequence IDs.')
for record in records:
ne... | Given a set of sequences, insert a prefix for each sequence's name. | entailment |
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: '
'including only IDs matching ' + filter_regex +
... | Given a set of sequences, filter out any sequences with names
that do not match the specified regular expression. Ignore case. | entailment |
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... | 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
description, then set the ID from the first word. If the ID and
the ... | entailment |
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 | Filter any sequences who's seq does not match the filter. Ignore case. | entailment |
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... | 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()`` | entailment |
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: '
'limiting results to top ' + head + ' records.')
if head == '-0':
for record in records:
yi... | Limit results to the top N records.
With the leading `-', print all but the last N records. | entailment |
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... | Limit results to the bottom N records.
Use +N to output records starting with the Nth. | entailment |
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... | Generates a list with the proportion of gaps by index in a set of
sequences. | entailment |
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())
... | 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. | entailment |
def strip_range(records):
"""
Cut off trailing /<start>-<stop> ranges from IDs. Ranges must be 1-indexed and
the stop integer must not be less than the start integer.
"""
logging.info('Applying _strip_range generator: '
'removing /<start>-<stop> ranges from IDs')
# Split up and... | Cut off trailing /<start>-<stop> ranges from IDs. Ranges must be 1-indexed and
the stop integer must not be less than the start integer. | entailment |
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... | Perform transcription or back-transcription.
transcribe must be one of the following:
dna2rna
rna2dna | entailment |
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... | 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:
dna2protein
dna2proteinstop
rna2prot... | entailment |
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:
... | Discard any records that are longer than max_length. | entailment |
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:
... | Discard any records that are shorter than min_length. | entailment |
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 | Discard any records that are shorter than min_length after removing gaps. | entailment |
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... | Sort sequences by length. 1 is ascending (default) and 0 is descending. | entailment |
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 | Return items from iterable in chunk_size bits.
If len(iterable) % chunk_size > 0, the last item returned will be shorter. | entailment |
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... | Run | entailment |
def _validate_translation(self, aligned_prot, aligned_nucl):
"""
Given a seq for protein and nucleotide, ensure that the translation holds
"""
codons = [''.join(i) for i in batch(str(aligned_nucl), 3)]
for codon, aa in zip(codons, str(aligned_prot)):
# Check gaps
... | Given a seq for protein and nucleotide, ensure that the translation holds | entailment |
def map_alignment(self, prot_seq, nucl_seq):
"""
Use aligned prot_seq to align nucl_seq
"""
if prot_seq.id != nucl_seq.id:
logging.warning(
'ID mismatch: %s != %s. Are the sequences in the same order?',
prot_seq.id, nucl_seq.id)
# Unga... | Use aligned prot_seq to align nucl_seq | entailment |
def map_all(self, prot_alignment, nucl_sequences):
"""
Convert protein sequences to nucleotide alignment
"""
zipped = itertools.zip_longest(prot_alignment, nucl_sequences)
for p, n in zipped:
if p is None:
raise ValueError("Exhausted protein sequences"... | Convert protein sequences to nucleotide alignment | entailment |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.