1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438
|
#!/usr/bin/env python3
"""
Multiple aligns sequence fields
"""
# Info
__author__ = 'Jason Anthony Vander Heiden'
from changeo import __version__, __date__
# Imports
import os
import shutil
from argparse import ArgumentParser
from collections import OrderedDict
from itertools import chain
from textwrap import dedent
from Bio.SeqRecord import SeqRecord
# Presto and changeo import
from presto.Defaults import default_out_args, default_muscle_exec
from presto.Applications import runMuscle
from presto.IO import printLog, printError, printWarning
from presto.Multiprocessing import manageProcesses
from changeo.Commandline import CommonHelpFormatter, checkArgs, getCommonArgParser, parseCommonArgs
from changeo.IO import getDbFields, getFormatOperators
from changeo.Multiprocessing import DbResult, feedDbQueue, processDbQueue, collectDbQueue
# TODO: maybe not bothering with 'set' is best. can just work off field identity
def groupRecords(records, fields=None, calls=['v', 'j'], mode='gene', action='first'):
"""
Groups Receptor objects based on gene or annotation
Arguments:
records : an iterator of Receptor objects to group.
fields : gene field to group by.
calls : allele calls to use for grouping.
one or more of ('v', 'd', 'j').
mode : specificity of alignment call to use for allele call fields.
one of ('allele', 'gene').
action : only 'first' is currently supported.
Returns:
dictionary of grouped records
"""
# Define functions for grouping keys
if mode == 'allele' and fields is None:
def _get_key(rec, calls, action):
return tuple(rec.getAlleleCalls(calls, action))
elif mode == 'gene' and fields is None:
def _get_key(rec, calls, action):
return tuple(rec.getGeneCalls(calls, action))
elif mode == 'allele' and fields is not None:
def _get_key(rec, calls, action):
vdj = rec.getAlleleCalls(calls, action)
ann = [rec.getChangeo(k) for k in fields]
return tuple(chain(vdj, ann))
elif mode == 'gene' and fields is not None:
def _get_key(rec, calls, action):
vdj = rec.getGeneCalls(calls, action)
ann = [rec.getChangeo(k) for k in fields]
return tuple(chain(vdj, ann))
rec_index = {}
for rec in records:
key = _get_key(rec, calls, action)
# Assigned grouped records to individual keys and all failed to a single key
if all([k is not None for k in key]):
rec_index.setdefault(key, []).append(rec)
else:
rec_index.setdefault(None, []).append(rec)
return rec_index
def alignBlocks(data, field_map, muscle_exec=default_muscle_exec):
"""
Multiple aligns blocks of sequence fields together
Arguments:
data : DbData object with Receptor objects to process.
field_map : a dictionary of {input sequence : output sequence) field names to multiple align.
muscle_exec : the MUSCLE executable.
Returns:
changeo.Multiprocessing.DbResult : object containing Receptor objects with multiple aligned sequence fields.
"""
# Define return object
result = DbResult(data.id, data.data)
result.results = data.data
result.valid = True
# Fail invalid groups
if result.id is None:
result.log = None
result.valid = False
return result
seq_fields = list(field_map.keys())
seq_list = [SeqRecord(r.getSeq(f), id='%s_%s' % (r.sequence_id.replace(' ', '_'), f)) for f in seq_fields \
for r in data.data]
seq_aln = runMuscle(seq_list, aligner_exec=muscle_exec)
if seq_aln is not None:
aln_map = {x.id: i for i, x in enumerate(seq_aln)}
for i, r in enumerate(result.results, start=1):
for f in seq_fields:
idx = aln_map['%s_%s' % (r.sequence_id.replace(' ', '_'), f)]
seq = str(seq_aln[idx].seq)
r.annotations[field_map[f]] = seq
result.log['%s-%s' % (f, r.sequence_id)] = seq
else:
result.valid = False
#for r in result.results: print r.annotations
return result
def alignAcross(data, field_map, muscle_exec=default_muscle_exec):
"""
Multiple aligns sequence fields column wise
Arguments:
data : DbData object with Receptor objects to process.
field_map : a dictionary of {input sequence : output sequence) field names to multiple align.
muscle_exec : the MUSCLE executable.
Returns:
changeo.Multiprocessing.DbResult : object containing Receptor objects with multiple aligned sequence fields.
"""
# Define return object
result = DbResult(data.id, data.data)
result.results = data.data
result.valid = True
# Fail invalid groups
if result.id is None:
result.log = None
result.valid = False
return result
seq_fields = list(field_map.keys())
for f in seq_fields:
seq_list = [SeqRecord(r.getSeq(f), id=r.sequence_id.replace(' ', '_')) for r in data.data]
seq_aln = runMuscle(seq_list, aligner_exec=muscle_exec)
if seq_aln is not None:
aln_map = {x.id: i for i, x in enumerate(seq_aln)}
for i, r in enumerate(result.results, start=1):
idx = aln_map[r.sequence_id.replace(' ', '_')]
seq = str(seq_aln[idx].seq)
r.annotations[field_map[f]] = seq
result.log['%s-%s' % (f, r.sequence_id)] = seq
else:
result.valid = False
#for r in result.results: print r.annotations
return result
def alignWithin(data, field_map, muscle_exec=default_muscle_exec):
"""
Multiple aligns sequence fields within a row
Arguments:
data : DbData object with Receptor objects to process.
field_map : a dictionary of {input sequence : output sequence) field names to multiple align.
muscle_exec : the MUSCLE executable.
Returns:
changeo.Multiprocessing.DbResult : object containing Receptor objects with multiple aligned sequence fields.
"""
# Define return object
result = DbResult(data.id, data.data)
result.results = data.data
result.valid = True
# Fail invalid groups
if result.id is None:
result.log = None
result.valid = False
return result
record = data.data
seq_fields = list(field_map.keys())
seq_list = [SeqRecord(record.getSeq(f), id=f) for f in seq_fields]
seq_aln = runMuscle(seq_list, aligner_exec=muscle_exec)
if seq_aln is not None:
aln_map = {x.id: i for i, x in enumerate(seq_aln)}
for f in seq_fields:
idx = aln_map[f]
seq = str(seq_aln[idx].seq)
record.annotations[field_map[f]] = seq
result.log[f] = seq
else:
result.valid = False
return result
def alignRecords(db_file, seq_fields, group_func, align_func, group_args={}, align_args={},
format='changeo', out_file=None, out_args=default_out_args, nproc=None, queue_size=None):
"""
Performs a multiple alignment on sets of sequences
Arguments:
db_file : filename of the input database.
seq_fields : the sequence fields to multiple align.
group_func : function to use to group records.
align_func : function to use to multiple align sequence groups.
group_args : dictionary of arguments to pass to group_func.
align_args : dictionary of arguments to pass to align_func.
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.
nproc : the number of processQueue processes.
if None defaults to the number of CPUs.
queue_size : maximum size of the argument queue.
if None defaults to 2*nproc.
Returns:
dict : names of the 'pass' and 'fail' output files.
"""
# Define subcommand label dictionary
cmd_dict = {alignAcross: 'across', alignWithin: 'within', alignBlocks: 'block'}
# Print parameter info
log = OrderedDict()
log['START'] = 'AlignRecords'
log['COMMAND'] = cmd_dict.get(align_func, align_func.__name__)
log['FILE'] = os.path.basename(db_file)
log['SEQ_FIELDS'] = ','.join(seq_fields)
if 'group_fields' in group_args: log['GROUP_FIELDS'] = ','.join(group_args['group_fields'])
if 'mode' in group_args: log['MODE'] = group_args['mode']
if 'action' in group_args: log['ACTION'] = group_args['action']
log['NPROC'] = nproc
printLog(log)
# Define format operators
try:
reader, writer, schema = getFormatOperators(format)
except ValueError:
printError('Invalid format %s.' % format)
# Define feeder function and arguments
if 'group_fields' in group_args and group_args['group_fields'] is not None:
group_args['group_fields'] = [schema.toReceptor(f) for f in group_args['group_fields']]
feed_func = feedDbQueue
feed_args = {'db_file': db_file,
'reader': reader,
'group_func': group_func,
'group_args': group_args}
# Define worker function and arguments
field_map = OrderedDict([(schema.toReceptor(f), '%s_align' % f) for f in seq_fields])
align_args['field_map'] = field_map
work_func = processDbQueue
work_args = {'process_func': align_func,
'process_args': align_args}
# Define collector function and arguments
out_fields = getDbFields(db_file, add=list(field_map.values()), reader=reader)
out_args['out_type'] = schema.out_type
collect_func = collectDbQueue
collect_args = {'db_file': db_file,
'label': 'align',
'fields': out_fields,
'writer': writer,
'out_file': out_file,
'out_args': out_args}
# Call process manager
result = manageProcesses(feed_func, work_func, collect_func,
feed_args, work_args, collect_args,
nproc, queue_size)
# Print log
result['log']['END'] = 'AlignRecords'
printLog(result['log'])
output = {k: v for k, v in result.items() if k in ('pass', 'fail')}
return output
def getArgParser():
"""
Defines the ArgumentParser
Arguments:
None
Returns:
an ArgumentParser object
"""
# Define output file names and header fields
fields = dedent(
'''
output files:
align-pass
database with multiple aligned sequences.
align-fail
database with records failing alignment.
required fields:
SEQUENCE_ID, V_CALL, J_CALL
<field>
user specified sequence fields to align.
output fields:
<field>_ALIGN
''')
# 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', metavar='',
help='alignment method')
# TODO: This is a temporary fix for Python issue 9253
subparsers.required = True
# Parent parser
parser_parent = getCommonArgParser(format=False, multiproc=True)
# Argument parser for column-wise alignment across records
parser_across = subparsers.add_parser('across', parents=[parser_parent],
formatter_class=CommonHelpFormatter, add_help=False,
help='''Multiple aligns sequence columns within groups
and across rows using MUSCLE.''')
group_across = parser_across.add_argument_group('alignment arguments')
group_across.add_argument('--sf', nargs='+', action='store', dest='seq_fields', required=True,
help='The sequence fields to multiple align within each group.')
group_across.add_argument('--gf', nargs='+', action='store', dest='group_fields', default=None,
help='Additional (not allele call) fields to use for grouping.')
group_across.add_argument('--calls', nargs='+', action='store', dest='calls',
choices=('v', 'd', 'j'), default=['v', 'j'],
help='Segment calls (allele assignments) to use for grouping.')
group_across.add_argument('--mode', action='store', dest='mode',
choices=('allele', 'gene'), default='gene',
help='''Specifies whether to use the V(D)J allele or gene when
an allele call field (--calls) is specified.''')
group_across.add_argument('--act', action='store', dest='action', default='first',
choices=('first', ),
help='''Specifies how to handle multiple values within default
allele call fields. Currently, only "first" is supported.''')
group_across.add_argument('--exec', action='store', dest='muscle_exec',
default=default_muscle_exec,
help='The location of the MUSCLE executable')
parser_across.set_defaults(group_func=groupRecords, align_func=alignAcross)
# Argument parser for alignment of fields within records
parser_within = subparsers.add_parser('within', parents=[parser_parent],
formatter_class=CommonHelpFormatter, add_help=False,
help='Multiple aligns sequence fields within rows using MUSCLE')
group_within = parser_within.add_argument_group('alignment arguments')
group_within.add_argument('--sf', nargs='+', action='store', dest='seq_fields', required=True,
help='The sequence fields to multiple align within each record.')
group_within.add_argument('--exec', action='store', dest='muscle_exec',
default=default_muscle_exec,
help='The location of the MUSCLE executable')
parser_within.set_defaults(group_func=None, align_func=alignWithin)
# Argument parser for column-wise alignment across records
parser_block = subparsers.add_parser('block', parents=[parser_parent],
formatter_class=CommonHelpFormatter, add_help=False,
help='''Multiple aligns sequence groups across both
columns and rows using MUSCLE.''')
group_block = parser_block.add_argument_group('alignment arguments')
group_block.add_argument('--sf', nargs='+', action='store', dest='seq_fields', required=True,
help='The sequence fields to multiple align within each group.')
group_block.add_argument('--gf', nargs='+', action='store', dest='group_fields', default=None,
help='Additional (not allele call) fields to use for grouping.')
group_block.add_argument('--calls', nargs='+', action='store', dest='calls',
choices=('v', 'd', 'j'), default=['v', 'j'],
help='Segment calls (allele assignments) to use for grouping.')
group_block.add_argument('--mode', action='store', dest='mode',
choices=('allele', 'gene'), default='gene',
help='''Specifies whether to use the V(D)J allele or gene when
an allele call field (--calls) is specified.''')
group_block.add_argument('--act', action='store', dest='action', default='first',
choices=('first', ),
help='''Specifies how to handle multiple values within default
allele call fields. Currently, only "first" is supported.''')
group_block.add_argument('--exec', action='store', dest='muscle_exec',
default=default_muscle_exec,
help='The location of the MUSCLE executable')
parser_block.set_defaults(group_func=groupRecords, align_func=alignBlocks)
return parser
if __name__ == '__main__':
"""
Parses command line arguments and calls main function
"""
# Parse arguments
parser = getArgParser()
checkArgs(parser)
args = parser.parse_args()
args_dict = parseCommonArgs(args)
# Convert case of fields
# if 'seq_fields' in args_dict:
# args_dict['seq_fields'] = [f.upper() for f in args_dict['seq_fields']]
# if 'group_fields' in args_dict and args_dict['group_fields'] is not None:
# args_dict['group_fields'] = [f.upper() for f in args_dict['group_fields']]
# Check if a valid MUSCLE executable was specified for muscle mode
if not shutil.which(args.muscle_exec):
parser.error('%s does not exist or is not executable.' % args.muscle_exec)
# Define align_args
args_dict['align_args'] = {'muscle_exec': args_dict['muscle_exec']}
del args_dict['muscle_exec']
# Define group_args
if args_dict['group_func'] is groupRecords:
args_dict['group_args'] = {'fields':args_dict['group_fields'],
'calls':args_dict['calls'],
'mode':args_dict['mode'],
'action':args_dict['action']}
del args_dict['group_fields']
del args_dict['calls']
del args_dict['mode']
del args_dict['action']
# Clean arguments dictionary
del args_dict['command']
del args_dict['db_files']
if 'out_files' in args_dict: del args_dict['out_files']
# Call main function for each input file
for i, f in enumerate(args.__dict__['db_files']):
args_dict['db_file'] = f
args_dict['out_file'] = args.__dict__['out_files'][i] \
if args.__dict__['out_files'] else None
alignRecords(**args_dict)
|