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
|
#!/usr/bin/env python3
"""
Assign V(D)J gene annotations
"""
# 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 pkg_resources import parse_version
from textwrap import dedent
from time import time
import re
import Bio
from Bio import SeqIO
# Presto imports
from presto.IO import printLog, printMessage, printError, printWarning
from changeo.Defaults import default_igblastn_exec, default_igblastp_exec, default_out_args
from changeo.Applications import runIgBLASTN, runIgBLASTP, getIgBLASTVersion
from changeo.Commandline import CommonHelpFormatter, checkArgs, getCommonArgParser, parseCommonArgs
from changeo.IO import getOutputName
# Defaults
choices_format = ('blast', 'airr')
choices_loci = ('ig', 'tr')
choices_organism = ('human', 'mouse', 'rabbit', 'rat', 'rhesus_monkey')
default_format = 'blast'
default_loci = 'ig'
default_organism = 'human'
default_igdata = '~/share/igblast'
def assignIgBLAST(seq_file, amino_acid=False, igdata=default_igdata, loci='ig', organism='human',
vdb=None, ddb=None, jdb=None, cdb=None, format=default_format,
igblast_exec=default_igblastn_exec, out_file=None,
out_args=default_out_args, nproc=None):
"""
Performs clustering on sets of sequences
Arguments:
seq_file (str): the sample sequence file name.
amino_acid : if True then run igblastp. igblastn is assumed if False.
igdata (str): path to the IgBLAST database directory (IGDATA environment).
loci (str): receptor type; one of 'ig' or 'tr'.
organism (str): species name.
vdb (str): name of a custom V reference in the database folder to use.
ddb (str): name of a custom D reference in the database folder to use.
jdb (str): name of a custom J reference in the database folder to use.
cdb (str): name of a custom C reference in the database folder to use.
format (str): output format. One of 'blast' or 'airr'.
exec (str): the path to the igblastn executable.
out_file (str): output file name. Automatically generated from the input file if None.
out_args (dict): common output argument dictionary from parseCommonArgs.
nproc (int): the number of processQueue processes;
if None defaults to the number of CPUs.
Returns:
str: the output file name
"""
# Check format argument
try:
out_type = {'blast': 'fmt7', 'airr': 'tsv'}[format]
except KeyError:
printError('Invalid output format %s.' % format)
# Get IgBLAST version
version = getIgBLASTVersion(exec=igblast_exec)
if parse_version(version) < parse_version('1.6'):
printError('IgBLAST version is %s and 1.6 or higher is required.' % version)
if format == 'airr' and parse_version(version) < parse_version('1.9'):
printError('IgBLAST version is %s and 1.9 or higher is required for AIRR format support.' % version)
# Print parameter info
log = OrderedDict()
log['START'] = 'AssignGenes'
log['COMMAND'] = 'igblast-aa' if amino_acid else 'igblast'
log['VERSION'] = version
log['FILE'] = os.path.basename(seq_file)
log['ORGANISM'] = organism
log['LOCI'] = loci
log['NPROC'] = nproc
printLog(log)
# Open output writer
if out_file is None:
out_file = getOutputName(seq_file, out_label='igblast', out_dir=out_args['out_dir'],
out_name=out_args['out_name'], out_type=out_type)
# convert to FASTA if needed
infile = open(seq_file, 'r')
test = infile.read()[0]
if test == "@":
printMessage("Running conversion from FASTQ to FASTA")
fasta_out_dir, filename = os.path.split(out_file)
out_fasta_file = os.path.split(seq_file)[1]
out_fasta_file = os.path.join(fasta_out_dir,'%s.fasta' % os.path.splitext(out_fasta_file)[0])
with open(out_fasta_file, "w") as out_handle:
records = SeqIO.parse(seq_file, 'fastq')
if parse_version(Bio.__version__) >= parse_version('1.71'):
# Biopython >= v1.71
SeqIO.write(records, out_handle, format='fasta-2line')
else:
# Biopython < v1.71
writer = SeqIO.FastaIO.FastaWriter(out_handle, wrap=None)
writer.write_file(records)
seq_file = out_fasta_file
# Run IgBLAST clustering
start_time = time()
printMessage('Running IgBLAST', start_time=start_time, width=25)
if not amino_acid:
console_out = runIgBLASTN(seq_file, igdata, loci=loci, organism=organism,
vdb=vdb, ddb=ddb, jdb=jdb, cdb=cdb, output=out_file,
format=format, threads=nproc, exec=igblast_exec)
else:
console_out = runIgBLASTP(seq_file, igdata, loci=loci, organism=organism,
vdb=vdb, output=out_file,
threads=nproc, exec=igblast_exec)
printMessage('Done', start_time=start_time, end=True, width=25)
# Get number of processed sequences
if (format == 'blast'):
with open(out_file, 'rb') as f:
f.seek(-2, os.SEEK_END)
while f.read(1) != b'\n':
f.seek(-2, os.SEEK_CUR)
pass_info = f.readline().decode()
num_seqs_match = re.search('(# BLAST processed )(\d+)( .*)', pass_info)
num_sequences = num_seqs_match.group(2)
else:
f = open(out_file, 'rb')
lines = 0
buf_size = 1024 * 1024
read_f = f.raw.read
buf = read_f(buf_size)
while buf:
lines += buf.count(b'\n')
buf = read_f(buf_size)
num_sequences = lines - 1
# Print log
log = OrderedDict()
log['PASS'] = num_sequences
log['OUTPUT'] = os.path.basename(out_file)
log['END'] = 'AssignGenes'
printLog(log)
return out_file
def getArgParser():
"""
Defines the ArgumentParser
Arguments:
None
Returns:
an ArgumentParser object
"""
# Define output file names and header fields
fields = dedent(
'''
output files:
igblast
Reference alignment results from IgBLAST.
''')
# 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='Assignment operation')
# TODO: This is a temporary fix for Python issue 9253
subparsers.required = True
# Parent parser
parent_parser = getCommonArgParser(db_in=False, log=False, failed=False, format=False, multiproc=True)
# Subparser to run igblastn
parser_igblast = subparsers.add_parser('igblast', parents=[parent_parser],
formatter_class=CommonHelpFormatter, add_help=False,
help='Executes igblastn.',
description='Executes igblastn.')
group_igblast = parser_igblast.add_argument_group('alignment arguments')
group_igblast.add_argument('-s', nargs='+', action='store', dest='seq_files', required=True,
help='A list of FASTA files containing sequences to process.')
group_igblast.add_argument('-b', action='store', dest='igdata', required=True,
help='IgBLAST database directory (IGDATA).')
group_igblast.add_argument('--organism', action='store', dest='organism', default=default_organism,
choices=choices_organism, help='Organism name.')
group_igblast.add_argument('--loci', action='store', dest='loci', default=default_loci,
choices=choices_loci, help='The receptor type.')
group_igblast.add_argument('--vdb', action='store', dest='vdb', default=None,
help='''Name of the custom V reference in the IgBLAST database folder.
If not specified, then a default database name with the form
imgt_<organism>_<loci>_v will be used.''')
group_igblast.add_argument('--ddb', action='store', dest='ddb', default=None,
help='''Name of the custom D reference in the IgBLAST database folder.
If not specified, then a default database name with the form
imgt_<organism>_<loci>_d will be used.''')
group_igblast.add_argument('--jdb', action='store', dest='jdb', default=None,
help='''Name of the custom J reference in the IgBLAST database folder.
If not specified, then a default database name with the form
imgt_<organism>_<loci>_j will be used.''')
group_igblast.add_argument('--cdb', action='store', dest='cdb', default=None,
help='''Name of the custom C reference in the IgBLAST database folder.
If not specified, then a default database name with the form
imgt_<organism>_<loci>_c will be used. Note, this argument will be
ignored for IgBLAST versions below 1.18.0.''')
group_igblast.add_argument('--format', action='store', dest='format', default=default_format,
choices=choices_format,
help='''Specify the output format. The "blast" will result in
the IgBLAST "-outfmt 7 std qseq sseq btop" output format.
Specifying "airr" will output the AIRR TSV format provided by
the IgBLAST argument "-outfmt 19".''')
group_igblast.add_argument('--exec', action='store', dest='igblast_exec',
default=default_igblastn_exec,
help='Path to the igblastn executable.')
parser_igblast.set_defaults(func=assignIgBLAST, amino_acid=False)
# Subparser to run igblastp
parser_igblast_aa = subparsers.add_parser('igblast-aa', parents=[parent_parser],
formatter_class=CommonHelpFormatter, add_help=False,
help='Executes igblastp.',
description='Executes igblastp.')
group_igblast_aa = parser_igblast_aa.add_argument_group('alignment arguments')
group_igblast_aa.add_argument('-s', nargs='+', action='store', dest='seq_files', required=True,
help='A list of FASTA files containing sequences to process.')
group_igblast_aa.add_argument('-b', action='store', dest='igdata', required=True,
help='IgBLAST database directory (IGDATA).')
group_igblast_aa.add_argument('--organism', action='store', dest='organism', default=default_organism,
choices=choices_organism, help='Organism name.')
group_igblast_aa.add_argument('--loci', action='store', dest='loci', default=default_loci,
choices=choices_loci, help='The receptor type.')
group_igblast_aa.add_argument('--vdb', action='store', dest='vdb', default=None,
help='''Name of the custom V reference in the IgBLAST database folder.
If not specified, then a default database name with the form
imgt_aa_<organism>_<loci>_v will be used.''')
group_igblast_aa.add_argument('--exec', action='store', dest='igblast_exec',
default=default_igblastp_exec,
help='Path to the igblastp executable.')
parser_igblast_aa.set_defaults(func=assignIgBLAST, amino_acid=True, ddb=None, jdb=None, format='blast')
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)
# Check if a valid clustering executable was specified
if not shutil.which(args_dict['igblast_exec']):
parser.error('%s executable not found' % args_dict['igblast_exec'])
# Clean arguments dictionary
del args_dict['seq_files']
if 'out_files' in args_dict: del args_dict['out_files']
del args_dict['func']
del args_dict['command']
# Call main function for each input file
for i, f in enumerate(args.__dict__['seq_files']):
args_dict['seq_file'] = f
args_dict['out_file'] = args.__dict__['out_files'][i] \
if args.__dict__['out_files'] else None
args.func(**args_dict)
|
