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#!/usr/bin/env python3
"""
Create tab-delimited database file to store sequence alignment information
"""
# Info
__author__ = 'Namita Gupta, Jason Anthony Vander Heiden'
from changeo import __version__, __date__
# Imports
import os
import re
from argparse import ArgumentParser
from collections import OrderedDict
from textwrap import dedent
from time import time
from Bio import SeqIO
# Presto and changeo imports
from presto.Annotation import parseAnnotation
from presto.IO import countSeqFile, printLog, printMessage, printProgress, printError, printWarning, readSeqFile
from changeo.Defaults import default_format, default_out_args
from changeo.Commandline import CommonHelpFormatter, checkArgs, getCommonArgParser, parseCommonArgs
from changeo.Gene import buildGermline
from changeo.IO import countDbFile, extractIMGT, readGermlines, getFormatOperators, getOutputHandle, \
AIRRWriter, ChangeoWriter, IgBLASTReader, IMGTReader, IHMMuneReader
from changeo.Receptor import ChangeoSchema, AIRRSchema
def addGermline(receptor, references):
"""
Add full length germline to Receptor object
Arguments:
receptor (changeo.Receptor.Receptor): Receptor object to modify.
references (dict): dictionary of IMGT-gapped references sequences.
Returns:
changeo.Receptor.Receptor: modified Receptor with the germline_imgt attribute added.
"""
__, germlines, __ = buildGermline(receptor, references)
germline_seq = None if germlines is None else germlines['full']
receptor.setField('germline_imgt', germline_seq)
return receptor
def getIDforIMGT(seq_file):
"""
Create a sequence ID translation using IMGT truncation.
Arguments:
seq_file : a fasta file of sequences input to IMGT.
Returns:
dict : a dictionary of with the IMGT truncated ID as the key and the full sequence description as the value.
"""
# Create a sequence ID translation using IDs truncate up to space or 50 chars
ids = {}
for rec in readSeqFile(seq_file):
if len(rec.description) <= 50:
id_key = rec.description
else:
id_key = re.sub('\||\s|!|&|\*|<|>|\?', '_', rec.description[:50])
ids.update({id_key: rec.description})
return ids
def getSeqDict(seq_file):
"""
Create a dictionary from a sequence file.
Arguments:
seq_file : sequence file.
Returns:
dict : sequence description as keys with Bio.SeqRecords as values.
"""
seq_dict = SeqIO.to_dict(readSeqFile(seq_file), key_function=lambda x: x.description)
return seq_dict
def writeDb(records, fields, aligner_file, total_count, id_dict=None, partial=False, asis_id=True,
writer=ChangeoWriter, out_file=None, out_args=default_out_args):
"""
Writes parsed records to an output file
Arguments:
records : a iterator of Receptor objects containing alignment data.
fields : a list of ordered field names to write.
aligner_file : input file name.
total_count : number of records (for progress bar).
id_dict : a dictionary of the truncated sequence ID mapped to the full sequence ID.
partial : if True put incomplete alignments in the pass file.
asis_id : if ID is to be parsed for pRESTO output with default delimiters.
writer : writer class.
out_file : output file name. Automatically generated from the input file if None.
out_args : common output argument dictionary from parseCommonArgs.
Returns:
None
"""
# Wrapper for opening handles and writers
def _open(x, f, writer=writer, out_file=out_file):
if out_file is not None and x == 'pass':
handle = open(out_file, 'w')
else:
handle = getOutputHandle(aligner_file,
out_label='db-%s' % x,
out_dir=out_args['out_dir'],
out_name=out_args['out_name'],
out_type=out_args['out_type'])
return handle, writer(handle, fields=f)
# Function to convert fasta header annotations to changeo columns
def _changeo(f, header):
h = [ChangeoSchema.fromReceptor(x) for x in header if x.upper() not in f]
f.extend(h)
return f
def _airr(f, header):
h = [AIRRSchema.fromReceptor(x) for x in header if x.lower() not in f]
f.extend(h)
return f
# Function to verify IMGT-gapped sequence and junction concur
def _imgt_check(rec):
try: check = (rec.junction == rec.sequence_imgt[309:(309 + rec.junction_length)])
except TypeError: check = False
return check
# Function to check for valid records strictly
def _strict(rec):
valid = [rec.v_call and rec.v_call != 'None',
rec.j_call and rec.j_call != 'None',
rec.functional is not None,
rec.sequence_imgt,
rec.junction,
_imgt_check(rec)]
return all(valid)
# Function to check for valid records loosely
def _gentle(rec):
valid = [rec.v_call and rec.v_call != 'None',
rec.d_call and rec.d_call != 'None',
rec.j_call and rec.j_call != 'None']
return any(valid)
# Set writer class and annotation conversion function
if writer == ChangeoWriter:
_annotate = _changeo
elif writer == AIRRWriter:
_annotate = _airr
else:
printError('Invalid output writer.')
# Set pass criteria
_pass = _gentle if partial else _strict
# Define log handle
if out_args['log_file'] is None:
log_handle = None
else:
log_handle = open(out_args['log_file'], 'w')
# Initialize handles, writers and counters
pass_handle, pass_writer = None, None
fail_handle, fail_writer = None, None
pass_count, fail_count = 0, 0
start_time = time()
# Validate and write output
printProgress(0, total_count, 0.05, start_time=start_time)
for i, record in enumerate(records, start=1):
# Replace sequence description with full string, if required
if id_dict is not None and record.sequence_id in id_dict:
record.sequence_id = id_dict[record.sequence_id]
# Parse sequence description into new columns
if not asis_id:
try:
ann_raw = parseAnnotation(record.sequence_id)
record.sequence_id = ann_raw.pop('ID')
# Convert to Receptor fields
ann_parsed = OrderedDict()
for k, v in ann_raw.items():
ann_parsed[ChangeoSchema.toReceptor(k)] = v
# If first record, use parsed description to define extra columns
if i == 1: fields = _annotate(fields, ann_parsed.keys())
# Update Receptor record
record.setDict(ann_parsed, parse=True)
except IndexError:
# Could not parse pRESTO-style annotations so fall back to no parse
asis_id = True
printWarning('Sequence annotation format not recognized. Sequence headers will not be parsed.')
# Count pass or fail and write to appropriate file
if _pass(record):
pass_count += 1
# Write row to pass file
try:
pass_writer.writeReceptor(record)
except AttributeError:
# Open pass file and writer
pass_handle, pass_writer = _open('pass', fields)
pass_writer.writeReceptor(record)
else:
fail_count += 1
# Write row to fail file if specified
if out_args['failed']:
try:
fail_writer.writeReceptor(record)
except AttributeError:
# Open fail file and writer
fail_handle, fail_writer = _open('fail', fields)
fail_writer.writeReceptor(record)
# Write log
if log_handle is not None:
log = OrderedDict([('ID', record.sequence_id),
('V_CALL', record.v_call),
('D_CALL', record.d_call),
('J_CALL', record.j_call),
('FUNCTIONAL', record.functional),
('IMGT_PASS', _imgt_check(record))])
printLog(log, log_handle)
# Print progress
printProgress(i, total_count, 0.05, start_time=start_time)
# Print consol log
log = OrderedDict()
log['OUTPUT'] = os.path.basename(pass_handle.name) if pass_handle is not None else None
log['PASS'] = pass_count
log['FAIL'] = fail_count
log['END'] = 'MakeDb'
printLog(log)
# Close file handles
output = {'pass': None, 'fail': None}
if pass_handle is not None:
output['pass'] = pass_handle.name
pass_handle.close()
if fail_handle is not None:
output['fail'] = fail_handle.name
fail_handle.close()
return output
def parseIMGT(aligner_file, seq_file=None, repo=None, partial=False, asis_id=True,
parse_scores=False, parse_regions=False, parse_junction=False,
format=default_format, out_file=None, out_args=default_out_args):
"""
Main for IMGT aligned sample sequences.
Arguments:
aligner_file : zipped file or unzipped folder output by IMGT.
seq_file : FASTA file input to IMGT (from which to get seqID).
repo : folder with germline repertoire files.
partial : If True put incomplete alignments in the pass file.
asis_id : if ID is to be parsed for pRESTO output with default delimiters.
parse_scores : if True add alignment score fields to output file.
parse_regions : if True add FWR and CDR region fields to output file.
format : output format. one of 'changeo' or 'airr'.
out_file : output file name. Automatically generated from the input file if None.
out_args : common output argument dictionary from parseCommonArgs.
Returns:
dict : names of the 'pass' and 'fail' output files.
"""
# Print parameter info
log = OrderedDict()
log['START'] = 'MakeDb'
log['ALIGNER'] = 'IMGT'
log['ALIGNER_FILE'] = aligner_file
log['SEQ_FILE'] = os.path.basename(seq_file) if seq_file else ''
log['ASIS_ID'] = asis_id
log['PARTIAL'] = partial
log['SCORES'] = parse_scores
log['REGIONS'] = parse_regions
log['JUNCTION'] = parse_junction
printLog(log)
start_time = time()
printMessage('Loading files', start_time=start_time, width=20)
# Extract IMGT files
temp_dir, imgt_files = extractIMGT(aligner_file)
# Count records in IMGT files
total_count = countDbFile(imgt_files['summary'])
# Get (parsed) IDs from fasta file submitted to IMGT
id_dict = getIDforIMGT(seq_file) if seq_file else {}
printMessage('Done', start_time=start_time, end=True, width=20)
# Define format operators
try:
__, writer, schema = getFormatOperators(format)
except ValueError:
printError('Invalid format %s.' % format)
out_args['out_type'] = schema.out_type
# Define output fields
fields = list(schema.standard_fields)
custom = IMGTReader.customFields(scores=parse_scores, regions=parse_regions,
junction=parse_junction, schema=schema)
fields.extend(custom)
# Parse IMGT output and write db
with open(imgt_files['summary'], 'r') as summary_handle, \
open(imgt_files['gapped'], 'r') as gapped_handle, \
open(imgt_files['ntseq'], 'r') as ntseq_handle, \
open(imgt_files['junction'], 'r') as junction_handle:
# Open parser
parse_iter = IMGTReader(summary_handle, gapped_handle, ntseq_handle, junction_handle)
# Add germline sequence
if repo is None:
germ_iter = parse_iter
else:
references = readGermlines(repo)
# Check for IMGT-gaps in germlines
if all('...' not in x for x in references.values()):
printWarning('Germline reference sequences do not appear to contain IMGT-numbering spacers. Results may be incorrect.')
germ_iter = (addGermline(x, references) for x in parse_iter)
# Write db
output = writeDb(germ_iter, fields=fields, aligner_file=aligner_file, total_count=total_count,
id_dict=id_dict, asis_id=asis_id, partial=partial,
writer=writer, out_file=out_file, out_args=out_args)
# Cleanup temp directory
temp_dir.cleanup()
return output
def parseIgBLAST(aligner_file, seq_file, repo, partial=False, asis_id=True, asis_calls=False,
parse_regions=False, parse_scores=False, parse_igblast_cdr3=False,
format='changeo', out_file=None, out_args=default_out_args):
"""
Main for IgBLAST aligned sample sequences.
Arguments:
aligner_file : IgBLAST output file to process.
seq_file : fasta file input to IgBlast (from which to get sequence).
repo : folder with germline repertoire files.
partial : If True put incomplete alignments in the pass file.
asis_id : if ID is to be parsed for pRESTO output with default delimiters.
asis_calls : if True do not parse gene calls for allele names.
parse_regions : if True add FWR and CDR fields to output file.
parse_scores : if True add alignment score fields to output file.
parse_igblast_cdr3 : if True parse CDR3 sequences generated by IgBLAST.
format : output format. one of 'changeo' or 'airr'.
out_file : output file name. Automatically generated from the input file if None.
out_args : common output argument dictionary from parseCommonArgs.
Returns:
dict : names of the 'pass' and 'fail' output files.
"""
# Print parameter info
log = OrderedDict()
log['START'] = 'MakeDB'
log['ALIGNER'] = 'IgBLAST'
log['ALIGNER_FILE'] = os.path.basename(aligner_file)
log['SEQ_FILE'] = os.path.basename(seq_file)
log['PARTIAL'] = partial
log['SCORES'] = parse_scores
log['REGIONS'] = parse_regions
log['ASIS_ID'] = asis_id
log['ASIS_CALLS'] = asis_calls
printLog(log)
start_time = time()
printMessage('Loading files', start_time=start_time, width=20)
# Count records in sequence file
total_count = countSeqFile(seq_file)
# Get input sequence dictionary
seq_dict = getSeqDict(seq_file)
# Create germline repo dictionary
references = readGermlines(repo, asis=asis_calls)
printMessage('Done', start_time=start_time, end=True, width=20)
# Check for IMGT-gaps in germlines
if all('...' not in x for x in references.values()):
printWarning('Germline reference sequences do not appear to contain IMGT-numbering spacers. Results may be incorrect.')
# Define format operators
try:
__, writer, schema = getFormatOperators(format)
except ValueError:
printError('Invalid format %s.' % format)
out_args['out_type'] = schema.out_type
# Define output fields
fields = list(schema.standard_fields)
custom = IgBLASTReader.customFields(scores=parse_scores, regions=parse_regions,
cdr3=parse_igblast_cdr3, schema=schema)
fields.extend(custom)
# Parse and write output
with open(aligner_file, 'r') as f:
parse_iter = IgBLASTReader(f, seq_dict, references, asis_calls=asis_calls)
germ_iter = (addGermline(x, references) for x in parse_iter)
output = writeDb(germ_iter, fields=fields, aligner_file=aligner_file, total_count=total_count,
partial=partial, asis_id=asis_id,
writer=writer, out_file=out_file, out_args=out_args)
return output
def parseIHMM(aligner_file, seq_file, repo, partial=False, asis_id=True,
parse_scores=False, parse_regions=False,
format=default_format, out_file=None, out_args=default_out_args):
"""
Main for iHMMuneAlign aligned sample sequences.
Arguments:
aligner_file : iHMMune-Align output file to process.
seq_file : fasta file input to iHMMuneAlign (from which to get sequence).
repo : folder with germline repertoire files.
partial : If True put incomplete alignments in the pass file.
parse_scores : if True parse alignment scores.
parse_regions : if True add FWR and CDR region fields.
asis_id : if ID is to be parsed for pRESTO output with default delimiters.
format : output format. One of 'changeo' or 'airr'.
out_file : output file name. Automatically generated from the input file if None.
out_args : common output argument dictionary from parseCommonArgs.
Returns:
dict : names of the 'pass' and 'fail' output files.
"""
# Print parameter info
log = OrderedDict()
log['START'] = 'MakeDB'
log['ALIGNER'] = 'iHMMune-Align'
log['ALIGNER_FILE'] = os.path.basename(aligner_file)
log['SEQ_FILE'] = os.path.basename(seq_file)
log['ASIS_ID'] = asis_id
log['PARTIAL'] = partial
log['SCORES'] = parse_scores
log['REGIONS'] = parse_regions
printLog(log)
start_time = time()
printMessage('Loading files', start_time=start_time, width=20)
# Count records in sequence file
total_count = countSeqFile(seq_file)
# Get input sequence dictionary
seq_dict = getSeqDict(seq_file)
# Create germline repo dictionary
references = readGermlines(repo)
printMessage('Done', start_time=start_time, end=True, width=20)
# Check for IMGT-gaps in germlines
if all('...' not in x for x in references.values()):
printWarning('Germline reference sequences do not appear to contain IMGT-numbering spacers. Results may be incorrect.')
# Define format operators
try:
__, writer, schema = getFormatOperators(format)
except ValueError:
printError('Invalid format %s.' % format)
out_args['out_type'] = schema.out_type
# Define output fields
fields = list(schema.standard_fields)
custom = IHMMuneReader.customFields(scores=parse_scores, regions=parse_regions,
schema=schema)
fields.extend(custom)
# Parse and write output
with open(aligner_file, 'r') as f:
parse_iter = IHMMuneReader(f, seq_dict, references)
germ_iter = (addGermline(x, references) for x in parse_iter)
output = writeDb(germ_iter, fields=fields, aligner_file=aligner_file, total_count=total_count,
asis_id=asis_id, partial=partial,
writer=writer, out_file=out_file, out_args=out_args)
return output
def getArgParser():
"""
Defines the ArgumentParser.
Returns:
argparse.ArgumentParser
"""
fields = dedent(
'''
output files:
db-pass
database of alignment records with functionality information,
V and J calls, and a junction region.
db-fail
database with records that fail due to no functionality information
(did not pass IMGT), no V call, no J call, or no junction region.
universal output fields:
SEQUENCE_ID, SEQUENCE_INPUT, SEQUENCE_VDJ, SEQUENCE_IMGT,
FUNCTIONAL, IN_FRAME, STOP, MUTATED_INVARIANT, INDELS,
V_CALL, D_CALL, J_CALL,
V_SEQ_START, V_SEQ_LENGTH,
D_SEQ_START, D_SEQ_LENGTH, D_GERM_START, D_GERM_LENGTH,
J_SEQ_START, J_SEQ_LENGTH, J_GERM_START, J_GERM_LENGTH,
NP1_LENGTH, NP2_LENGTH,
JUNCTION_LENGTH, JUNCTION, GERMLINE_IMGT,
FWR1_IMGT, FWR2_IMGT, FWR3_IMGT, FWR4_IMGT,
CDR1_IMGT, CDR2_IMGT, CDR3_IMGT
imgt specific output fields:
V_GERM_START_IMGT, V_GERM_LENGTH_IMGT,
N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH, P5J_LENGTH,
D_FRAME, V_SCORE, V_IDENTITY, J_SCORE, J_IDENTITY,
igblast specific output fields:
V_GERM_START_VDJ, V_GERM_LENGTH_VDJ,
V_EVALUE, V_SCORE, V_IDENTITY, V_CIGAR,
D_EVALUE, D_SCORE, D_IDENTITY, D_CIGAR,
J_EVALUE, J_SCORE, J_IDENTITY, J_CIGAR,
CDR3_IGBLAST, CDR3_IGBLAST_AA
ihmm specific output fields:
V_GERM_START_VDJ, V_GERM_LENGTH_VDJ, VDJ_SCORE
''')
# Define ArgumentParser
parser = ArgumentParser(description=__doc__, epilog=fields,
formatter_class=CommonHelpFormatter, add_help=False)
group_help = parser.add_argument_group('help')
group_help.add_argument('--version', action='version',
version='%(prog)s:' + ' %s %s' %(__version__, __date__))
group_help.add_argument('-h', '--help', action='help', help='show this help message and exit')
subparsers = parser.add_subparsers(title='subcommands', dest='command',
help='Aligner used', metavar='')
# TODO: This is a temporary fix for Python issue 9253
subparsers.required = True
# Parent parser
parser_parent = getCommonArgParser(db_in=False)
# IgBlast Aligner
parser_igblast = subparsers.add_parser('igblast', parents=[parser_parent],
formatter_class=CommonHelpFormatter, add_help=False,
help='Process IgBLAST output.',
description='Process IgBLAST output.')
group_igblast = parser_igblast.add_argument_group('aligner parsing arguments')
group_igblast.add_argument('-i', nargs='+', action='store', dest='aligner_files',
required=True,
help='''IgBLAST output files in format 7 with query sequence
(IgBLAST argument \'-outfmt "7 std qseq sseq btop"\').''')
group_igblast.add_argument('-r', nargs='+', action='store', dest='repo', required=True,
help='''List of folders and/or fasta files containing
the same germline set used in the IgBLAST alignment. These
reference sequences must contain IMGT-numbering spacers (gaps)
in the V segment.''')
group_igblast.add_argument('-s', action='store', nargs='+', dest='seq_files',
required=True,
help='''List of input FASTA files (with .fasta, .fna or .fa
extension), containing sequences.''')
group_igblast.add_argument('--partial', action='store_true', dest='partial',
help='''If specified, include incomplete V(D)J alignments in
the pass file instead of the fail file. An incomplete alignment
is defined as a record for which a valid IMGT-gapped sequence
cannot be built or that is missing a V gene assignment,
J gene assignment, junction region, or productivity call.''')
group_igblast.add_argument('--scores', action='store_true', dest='parse_scores',
help='''Specify if alignment score metrics should be
included in the output. Adds the <VDJ>_SCORE, <VDJ>_IDENTITY,
<VDJ>_EVALUE, <VDJ>_CIGAR columns.''')
group_igblast.add_argument('--regions', action='store_true', dest='parse_regions',
help='''Specify if IMGT FWR and CDRs should be
included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
CDR3_IMGT columns.''')
group_igblast.add_argument('--cdr3', action='store_true',
dest='parse_igblast_cdr3',
help='''Specify if the CDR3 sequences generated by IgBLAST
should be included in the output. Adds the columns
CDR3_IGBLAST_NT and CDR3_IGBLAST_AA. Requires IgBLAST
version 1.5 or greater.''')
group_igblast.add_argument('--asis-id', action='store_true', dest='asis_id',
help='''Specify to prevent input sequence headers from being parsed
to add new columns to database. Parsing of sequence headers requires
headers to be in the pRESTO annotation format, so this should be specified
when sequence headers are incompatible with the pRESTO annotation scheme.
Note, unrecognized header formats will default to this behavior.''')
group_igblast.add_argument('--asis-calls', action='store_true', dest='asis_calls',
help='''Specify to prevent gene calls from being parsed into standard allele names
in both the IgBLAST output and reference database. Note, this requires
the sequence identifiers in the reference sequence set and the IgBLAST
database to be exact string matches.''')
parser_igblast.set_defaults(func=parseIgBLAST)
# IMGT aligner
parser_imgt = subparsers.add_parser('imgt', parents=[parser_parent],
formatter_class=CommonHelpFormatter, add_help=False,
help='''Process IMGT/HighV-Quest output
(does not work with V-QUEST).''',
description='''Process IMGT/HighV-Quest output
(does not work with V-QUEST).''')
group_imgt = parser_imgt.add_argument_group('aligner parsing arguments')
group_imgt.add_argument('-i', nargs='+', action='store', dest='aligner_files',
help='''Either zipped IMGT output files (.zip or .txz) or a
folder containing unzipped IMGT output files (which must
include 1_Summary, 2_IMGT-gapped, 3_Nt-sequences,
and 6_Junction).''')
group_imgt.add_argument('-s', nargs='*', action='store', dest='seq_files', required=False,
help='''List of FASTA files (with .fasta, .fna or .fa
extension) that were submitted to IMGT/HighV-QUEST.
If unspecified, sequence identifiers truncated by IMGT/HighV-QUEST
will not be corrected.''')
group_imgt.add_argument('-r', nargs='+', action='store', dest='repo', required=False,
help='''List of folders and/or fasta files containing
the germline sequence set used by IMGT/HighV-QUEST.
These reference sequences must contain IMGT-numbering spacers (gaps)
in the V segment. If unspecified, the germline sequence reconstruction
will not be included in the output.''')
group_imgt.add_argument('--asis-id', action='store_true', dest='asis_id',
help='''Specify to prevent input sequence headers from being parsed
to add new columns to database. Parsing of sequence headers requires
headers to be in the pRESTO annotation format, so this should be specified
when sequence headers are incompatible with the pRESTO annotation scheme.
Note, unrecognized header formats will default to this behavior.''')
group_imgt.add_argument('--partial', action='store_true', dest='partial',
help='''If specified, include incomplete V(D)J alignments in
the pass file instead of the fail file. An incomplete alignment
is defined as a record that is missing a V gene assignment,
J gene assignment, junction region, or productivity call.''')
group_imgt.add_argument('--scores', action='store_true', dest='parse_scores',
help='''Specify if alignment score metrics should be
included in the output. Adds the <VDJ>_SCORE and
<VDJ>_IDENTITY> columns.''')
group_imgt.add_argument('--regions', action='store_true', dest='parse_regions',
help='''Specify if IMGT FWRs and CDRs should be
included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
CDR3_IMGT columns.''')
group_imgt.add_argument('--junction', action='store_true', dest='parse_junction',
help='''Specify if detailed junction fields should be
included in the output. Adds the columns
N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH,
P5J_LENGTH, D_FRAME.''')
parser_imgt.set_defaults(func=parseIMGT)
# iHMMuneAlign Aligner
parser_ihmm = subparsers.add_parser('ihmm', parents=[parser_parent],
formatter_class=CommonHelpFormatter, add_help=False,
help='Process iHMMune-Align output.',
description='Process iHMMune-Align output.')
group_ihmm = parser_ihmm.add_argument_group('aligner parsing arguments')
group_ihmm.add_argument('-i', nargs='+', action='store', dest='aligner_files',
required=True,
help='''iHMMune-Align output file.''')
group_ihmm.add_argument('-r', nargs='+', action='store', dest='repo', required=True,
help='''List of folders and/or FASTA files containing
the set of germline sequences used by iHMMune-Align. These
reference sequences must contain IMGT-numbering spacers (gaps)
in the V segment.''')
group_ihmm.add_argument('-s', action='store', nargs='+', dest='seq_files',
required=True,
help='''List of input FASTA files (with .fasta, .fna or .fa
extension) containing sequences.''')
group_ihmm.add_argument('--asis-id', action='store_true', dest='asis_id',
help='''Specify to prevent input sequence headers from being parsed
to add new columns to database. Parsing of sequence headers requires
headers to be in the pRESTO annotation format, so this should be specified
when sequence headers are incompatible with the pRESTO annotation scheme.
Note, unrecognized header formats will default to this behavior.''')
group_ihmm.add_argument('--partial', action='store_true', dest='partial',
help='''If specified, include incomplete V(D)J alignments in
the pass file instead of the fail file. An incomplete alignment
is defined as a record for which a valid IMGT-gapped sequence
cannot be built or that is missing a V gene assignment,
J gene assignment, junction region, or productivity call.''')
group_ihmm.add_argument('--scores', action='store_true', dest='parse_scores',
help='''Specify if alignment score metrics should be
included in the output. Adds the path score of the
iHMMune-Align hidden Markov model to VDJ_SCORE.''')
group_ihmm.add_argument('--regions', action='store_true', dest='parse_regions',
help='''Specify if IMGT FWRs and CDRs should be
included in the output. Adds the FWR1_IMGT, FWR2_IMGT,
FWR3_IMGT, FWR4_IMGT, CDR1_IMGT, CDR2_IMGT, and
CDR3_IMGT columns.''')
parser_ihmm.set_defaults(func=parseIHMM)
return parser
if __name__ == "__main__":
"""
Parses command line arguments and calls main
"""
parser = getArgParser()
checkArgs(parser)
args = parser.parse_args()
args_dict = parseCommonArgs(args, in_arg='aligner_files')
# Set no ID parsing if sequence files are not provided
if 'seq_files' in args_dict and not args_dict['seq_files']:
args_dict['asis_id'] = True
# Delete
if 'aligner_files' in args_dict: del args_dict['aligner_files']
if 'seq_files' in args_dict: del args_dict['seq_files']
if 'out_files' in args_dict: del args_dict['out_files']
if 'command' in args_dict: del args_dict['command']
if 'func' in args_dict: del args_dict['func']
# Call main
for i, f in enumerate(args.__dict__['aligner_files']):
args_dict['aligner_file'] = f
args_dict['seq_file'] = args.__dict__['seq_files'][i] \
if args.__dict__['seq_files'] else None
args_dict['out_file'] = args.__dict__['out_files'][i] \
if args.__dict__['out_files'] else None
args.func(**args_dict)
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