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broadinstitute/fiss | firecloud/fiss.py | space_lock | def space_lock(args):
""" Lock a workspace """
r = fapi.lock_workspace(args.project, args.workspace)
fapi._check_response_code(r, 204)
if fcconfig.verbosity:
eprint('Locked workspace {0}/{1}'.format(args.project, args.workspace))
return 0 | python | def space_lock(args):
""" Lock a workspace """
r = fapi.lock_workspace(args.project, args.workspace)
fapi._check_response_code(r, 204)
if fcconfig.verbosity:
eprint('Locked workspace {0}/{1}'.format(args.project, args.workspace))
return 0 | [
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broadinstitute/fiss | firecloud/fiss.py | space_unlock | def space_unlock(args):
""" Unlock a workspace """
r = fapi.unlock_workspace(args.project, args.workspace)
fapi._check_response_code(r, 204)
if fcconfig.verbosity:
eprint('Unlocked workspace {0}/{1}'.format(args.project,args.workspace))
return 0 | python | def space_unlock(args):
""" Unlock a workspace """
r = fapi.unlock_workspace(args.project, args.workspace)
fapi._check_response_code(r, 204)
if fcconfig.verbosity:
eprint('Unlocked workspace {0}/{1}'.format(args.project,args.workspace))
return 0 | [
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broadinstitute/fiss | firecloud/fiss.py | space_new | def space_new(args):
""" Create a new workspace. """
r = fapi.create_workspace(args.project, args.workspace,
args.authdomain, dict())
fapi._check_response_code(r, 201)
if fcconfig.verbosity:
eprint(r.content)
return 0 | python | def space_new(args):
""" Create a new workspace. """
r = fapi.create_workspace(args.project, args.workspace,
args.authdomain, dict())
fapi._check_response_code(r, 201)
if fcconfig.verbosity:
eprint(r.content)
return 0 | [
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broadinstitute/fiss | firecloud/fiss.py | space_info | def space_info(args):
""" Get metadata for a workspace. """
r = fapi.get_workspace(args.project, args.workspace)
fapi._check_response_code(r, 200)
return r.text | python | def space_info(args):
""" Get metadata for a workspace. """
r = fapi.get_workspace(args.project, args.workspace)
fapi._check_response_code(r, 200)
return r.text | [
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broadinstitute/fiss | firecloud/fiss.py | space_delete | def space_delete(args):
""" Delete a workspace. """
message = "WARNING: this will delete workspace: \n\t{0}/{1}".format(
args.project, args.workspace)
if not args.yes and not _confirm_prompt(message):
return 0
r = fapi.delete_workspace(args.project, args.workspace)
fapi._check_respo... | python | def space_delete(args):
""" Delete a workspace. """
message = "WARNING: this will delete workspace: \n\t{0}/{1}".format(
args.project, args.workspace)
if not args.yes and not _confirm_prompt(message):
return 0
r = fapi.delete_workspace(args.project, args.workspace)
fapi._check_respo... | [
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broadinstitute/fiss | firecloud/fiss.py | space_clone | def space_clone(args):
""" Replicate a workspace """
# FIXME: add --deep copy option (shallow by default)
# add aliasing capability, then make space_copy alias
if not args.to_workspace:
args.to_workspace = args.workspace
if not args.to_project:
args.to_project = args.project
... | python | def space_clone(args):
""" Replicate a workspace """
# FIXME: add --deep copy option (shallow by default)
# add aliasing capability, then make space_copy alias
if not args.to_workspace:
args.to_workspace = args.workspace
if not args.to_project:
args.to_project = args.project
... | [
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broadinstitute/fiss | firecloud/fiss.py | space_acl | def space_acl(args):
''' Retrieve access control list for a workspace'''
r = fapi.get_workspace_acl(args.project, args.workspace)
fapi._check_response_code(r, 200)
result = dict()
for user, info in sorted(r.json()['acl'].items()):
result[user] = info['accessLevel']
return result | python | def space_acl(args):
''' Retrieve access control list for a workspace'''
r = fapi.get_workspace_acl(args.project, args.workspace)
fapi._check_response_code(r, 200)
result = dict()
for user, info in sorted(r.json()['acl'].items()):
result[user] = info['accessLevel']
return result | [
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broadinstitute/fiss | firecloud/fiss.py | space_set_acl | def space_set_acl(args):
""" Assign an ACL role to list of users for a workspace """
acl_updates = [{"email": user,
"accessLevel": args.role} for user in args.users]
r = fapi.update_workspace_acl(args.project, args.workspace, acl_updates)
fapi._check_response_code(r, 200)
errors =... | python | def space_set_acl(args):
""" Assign an ACL role to list of users for a workspace """
acl_updates = [{"email": user,
"accessLevel": args.role} for user in args.users]
r = fapi.update_workspace_acl(args.project, args.workspace, acl_updates)
fapi._check_response_code(r, 200)
errors =... | [
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broadinstitute/fiss | firecloud/fiss.py | space_search | def space_search(args):
""" Search for workspaces matching certain criteria """
r = fapi.list_workspaces()
fapi._check_response_code(r, 200)
# Parse the JSON for workspace + namespace; then filter by
# search terms: each term is treated as a regular expression
workspaces = r.json()
extra_te... | python | def space_search(args):
""" Search for workspaces matching certain criteria """
r = fapi.list_workspaces()
fapi._check_response_code(r, 200)
# Parse the JSON for workspace + namespace; then filter by
# search terms: each term is treated as a regular expression
workspaces = r.json()
extra_te... | [
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broadinstitute/fiss | firecloud/fiss.py | entity_import | def entity_import(args):
""" Upload an entity loadfile. """
project = args.project
workspace = args.workspace
chunk_size = args.chunk_size
with open(args.tsvfile) as tsvf:
headerline = tsvf.readline().strip()
entity_data = [l.rstrip('\n') for l in tsvf]
return _batch_load(proje... | python | def entity_import(args):
""" Upload an entity loadfile. """
project = args.project
workspace = args.workspace
chunk_size = args.chunk_size
with open(args.tsvfile) as tsvf:
headerline = tsvf.readline().strip()
entity_data = [l.rstrip('\n') for l in tsvf]
return _batch_load(proje... | [
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broadinstitute/fiss | firecloud/fiss.py | entity_types | def entity_types(args):
""" List entity types in a workspace """
r = fapi.list_entity_types(args.project, args.workspace)
fapi._check_response_code(r, 200)
return r.json().keys() | python | def entity_types(args):
""" List entity types in a workspace """
r = fapi.list_entity_types(args.project, args.workspace)
fapi._check_response_code(r, 200)
return r.json().keys() | [
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broadinstitute/fiss | firecloud/fiss.py | entity_list | def entity_list(args):
""" List entities in a workspace. """
r = fapi.get_entities_with_type(args.project, args.workspace)
fapi._check_response_code(r, 200)
return [ '{0}\t{1}'.format(e['entityType'], e['name']) for e in r.json() ] | python | def entity_list(args):
""" List entities in a workspace. """
r = fapi.get_entities_with_type(args.project, args.workspace)
fapi._check_response_code(r, 200)
return [ '{0}\t{1}'.format(e['entityType'], e['name']) for e in r.json() ] | [
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broadinstitute/fiss | firecloud/fiss.py | participant_list | def participant_list(args):
''' List participants within a container'''
# Case 1: retrieve participants within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for participant within participant (itself)
if args.entity_type == 'participant':
ret... | python | def participant_list(args):
''' List participants within a container'''
# Case 1: retrieve participants within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for participant within participant (itself)
if args.entity_type == 'participant':
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broadinstitute/fiss | firecloud/fiss.py | pair_list | def pair_list(args):
''' List pairs within a container. '''
# Case 1: retrieve pairs within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for pair within a pair (itself)
if args.entity_type == 'pair':
return [ args.entity.strip() ]
# ... | python | def pair_list(args):
''' List pairs within a container. '''
# Case 1: retrieve pairs within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for pair within a pair (itself)
if args.entity_type == 'pair':
return [ args.entity.strip() ]
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broadinstitute/fiss | firecloud/fiss.py | sample_list | def sample_list(args):
''' List samples within a container. '''
# Case 1: retrieve samples within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for samples within a sample (itself)
if args.entity_type == 'sample':
return [ args.entity.strip()... | python | def sample_list(args):
''' List samples within a container. '''
# Case 1: retrieve samples within a named data entity
if args.entity_type and args.entity:
# Edge case: caller asked for samples within a sample (itself)
if args.entity_type == 'sample':
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broadinstitute/fiss | firecloud/fiss.py | entity_delete | 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,
... | python | def entity_delete(args):
""" Delete entity in a workspace. """
msg = "WARNING: this will delete {0} {1} in {2}/{3}".format(
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if not (args.yes or _confirm_prompt(msg)):
return
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broadinstitute/fiss | firecloud/fiss.py | meth_wdl | 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 | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | meth_acl | 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... | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | meth_set_acl | def meth_set_acl(args):
""" Assign an ACL role to a list of users for a workflow. """
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for user in set(expand_fc_groups(args.users)) \
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if not id:
# get the lat... | python | def meth_set_acl(args):
""" Assign an ACL role to a list of users for a workflow. """
acl_updates = [{"user": user, "role": args.role} \
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broadinstitute/fiss | firecloud/fiss.py | expand_fc_groups | 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... | python | 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:
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broadinstitute/fiss | firecloud/fiss.py | meth_list | 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... | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | config_acl | 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'])
... | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | config_set_acl | def config_set_acl(args):
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for user in set(expand_fc_groups(args.users)) \
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if not id:
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broadinstitute/fiss | firecloud/fiss.py | config_get | 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... | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | config_wdl | 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.... | python | 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)
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broadinstitute/fiss | firecloud/fiss.py | config_diff | 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
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"""Compare method configuration definitions across workspaces. Ignores
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config_1 = config_get(args).splitlines()
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broadinstitute/fiss | firecloud/fiss.py | config_delete | 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 | python | 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])
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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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""" Copy workspace attributes between workspaces. """
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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)
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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
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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'''
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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
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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
if (args.project == args.to_project
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ep... | python | 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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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 | _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)]: ",
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)
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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]
tsplit = first_col.split(':')
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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/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
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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:
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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 | moving_average | def moving_average(iterable, n):
"""
From Python collections module documentation
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"""
it = iter(iterable)
d = collections.deque(itertools.islice(it, n - 1))
d.appendleft(0)
s = sum(d)
for elem in it:
s += elem ... | python | def moving_average(iterable, n):
"""
From Python collections module documentation
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"""
it = iter(iterable)
d = collections.deque(itertools.islice(it, n - 1))
d.appendleft(0)
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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()
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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.
"""
if arguments.quality_window_mean_qual and not arguments.quality_window:
raise ValueError("--quality-window-mean-qual specified without "
"--quality-window")
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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):
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assert record.id == self.current_record['sequence_name']
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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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assert (filtered)
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fhcrc/seqmagick | seqmagick/subcommands/quality_filter.py | AmbiguousBaseFilter.filter_record | def filter_record(self, record):
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"""
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"""
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):
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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):
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Filter record, truncating any over some maximum length
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if len(record) >= self.max_length:
return record[:self.max_length]
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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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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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"""
with tempfile.SpooledTemporaryFile(buffer_size, mode='wb+')... | [
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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
-.
"""
logging.info(
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translation_table = {ord(c): '-' for c in prune_chars}
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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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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.
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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 | 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
"""
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try:
record = next(i for i in r() if i.id == record_id)
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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.
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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 | 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.')
for record in records:
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:
yield ungap_all(record, gap_chars) | [
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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):
"""
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"""
logging.info('Applying _name_append_suffix generator: '
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'sequence IDs.')
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.
"""
logging.info('Applying _name_append_suffix generator: '
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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: '
'Inserting prefix ' + prefix + ' for all '
'sequence IDs.')
for record in records:
ne... | python | 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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'sequence IDs.')
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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: '
'including only IDs matching ' + filter_regex +
... | python | 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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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
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
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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 | 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: '
'limiting results to top ' + head + ' records.')
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.
"""
logging.info('Applying _head generator: '
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if head == '-0':
for record in records:
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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: '
'limiting results to top ' + tail + ' records.')
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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
sequences.
"""
aln_len = None
gaps = []
for i, sequence in enumerate(sequences):
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gaps = [0] * aln_le... | [
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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
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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
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"""
with _record_buffer(records) as r:
gap_proportions = gap_proportion(r())
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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)
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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/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:
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fhcrc/seqmagick | seqmagick/subcommands/backtrans_align.py | AlignmentMapper._validate_translation | 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
... | python | 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)]
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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
"""
zipped = itertools.zip_longest(prot_alignment, nucl_sequences)
for p, n in zipped:
if p is None:
raise ValueError("Exhausted protein sequences"... | python | 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:
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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:
return EXTENSION_TO_TYPE[extension.lower()]
... | python | 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:
return EXTENSION_TO_TYPE[extension.lower()]
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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.
"""
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.
For stdin, stdout, and stderr, ``stream_default`` is used.
"""
if fh in (sys.stdin, sys.stdout, sys.stderr):
return stream_default
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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',
version='seqmagick v'... | [
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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 | _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',
'C': 'C',
'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 | 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)
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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
fileformat.from_handle(arguments.source_file))
output_format = (arguments.output_format or
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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``.
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``permissions``: Permissions to set (default: umask)
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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)
if not result >= minimum and result <= maximum:
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)
if not result >= minimum and result <= maximum:
raise argparse.Argume... | [
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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
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.
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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 | 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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phac-nml/sistr_cmd | sistr/src/parsers.py | parse_fasta | def parse_fasta(filepath):
'''
Parse a fasta file returning a generator yielding tuples of fasta headers to sequences.
Note:
This function should give equivalent results to SeqIO from BioPython
.. code-block:: python
from Bio import SeqIO
# biopython to dict of hea... | python | def parse_fasta(filepath):
'''
Parse a fasta file returning a generator yielding tuples of fasta headers to sequences.
Note:
This function should give equivalent results to SeqIO from BioPython
.. code-block:: python
from Bio import SeqIO
# biopython to dict of hea... | [
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Note:
This function should give equivalent results to SeqIO from BioPython
.. code-block:: python
from Bio import SeqIO
# biopython to dict of header-seq
hseqs_bio = {r.desc... | [
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phac-nml/sistr_cmd | sistr/src/parsers.py | fasta_format_check | def fasta_format_check(fasta_path, logger):
"""
Check that a file is valid FASTA format.
- First non-blank line needs to begin with a '>' header character.
- Sequence can only contain valid IUPAC nucleotide characters
Args:
fasta_str (str): FASTA file contents string
Raises:
... | python | def fasta_format_check(fasta_path, logger):
"""
Check that a file is valid FASTA format.
- First non-blank line needs to begin with a '>' header character.
- Sequence can only contain valid IUPAC nucleotide characters
Args:
fasta_str (str): FASTA file contents string
Raises:
... | [
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- First non-blank line needs to begin with a '>' header character.
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Args:
fasta_str (str): FASTA file contents string
Raises:
Exception: If invalid FASTA format | [
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