Skip to content

default ref databases tried will be airrc-imgt then imgt #233

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ssnn-airr wants to merge 1 commit into
base: master
Choose a base branch
from
Open

default ref databases tried will be airrc-imgt then imgt #233

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 15 additions & 11 deletions bin/AssignGenes.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -201,21 +201,24 @@ def getArgParser():
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.''')
If not specified, the database folder is searched for a file
matching airrc-imgt_<organism>_<loci>_v first, then imgt_<organism>_<loci>_v.
If neither is found, --vdb must be specified explicitly.''')
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.''')
If not specified, the database folder is searched for a file
matching airrc-imgt_<organism>_<loci>_d first, then imgt_<organism>_<loci>_d.
If neither is found, --ddb must be specified explicitly.''')
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.''')
If not specified, the database folder is searched for a file
matching airrc-imgt_<organism>_<loci>_j first, then imgt_<organism>_<loci>_j.
If neither is found, --jdb must be specified explicitly.''')
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.''')
If not specified, the database folder is searched for a file
matching airrc-imgt_<organism>_<loci>_c first, then imgt_<organism>_<loci>_c.
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
Expand Down Expand Up @@ -243,8 +246,9 @@ def getArgParser():
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.''')
If not specified, the database folder is searched for a file
matching airrc-imgt_aa_<organism>_<loci>_v first, then imgt_aa_<organism>_<loci>_v.
If neither is found, --vdb must be specified explicitly.''')
group_igblast_aa.add_argument('--exec', action='store', dest='igblast_exec',
default=default_igblastp_exec,
help='Path to the igblastp executable.')
Expand Down
66 changes: 55 additions & 11 deletions changeo/Applications.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
__author__ = 'Jason Anthony Vander Heiden'

# Imports
import glob
import os
import re
from packaging.version import parse as parse_version
Expand All @@ -20,6 +21,38 @@
default_igblast_output = 'legacy'


def _resolve_db(igdata, segment, organism, loci, explicit=None, aa=False):
"""
Resolve an IgBLAST database path by probing the filesystem.

Tries the 'airrc-imgt' prefix first, then 'imgt'. Returns None if neither is
found and no explicit name was given.

Arguments:
igdata (str): path to the IgBLAST database directory.
segment (str): gene segment; one of 'v', 'd', 'j', or 'c'.
organism (str): species name.
loci (str): receptor type; one of 'ig' or 'tr'.
explicit (str): explicit database name, bypassing prefix resolution.
aa (bool): if True, use the amino acid infix ('airrc-imgt_aa_' / 'imgt_aa_').

Returns:
str: full path to the database, or None if not found.
"""
if explicit is not None:
return os.path.join(igdata, 'database', explicit)

infix = '_aa_' if aa else '_'
db_dir = os.path.join(igdata, 'database')
for prefix in ('airrc-imgt', 'imgt'):
name = '%s%s%s_%s_%s' % (prefix, infix, organism, loci, segment)
path = os.path.join(db_dir, name)
if glob.glob(path + '.*') or os.path.isfile(path):
return path

return None


def runASN(fasta, template=None, exec=default_tbl2asn_exec):
"""
Executes tbl2asn to generate Sequin files
Expand Down Expand Up @@ -157,17 +190,26 @@ def runIgBLASTN(fasta, igdata, loci='ig', organism='human', vdb=None, ddb=None,
# Set auxiliary data
auxiliary = os.path.join(igdata, 'optional_file', '%s_gl.aux' % organism)
# Set V database
if vdb is not None: v_germ = os.path.join(igdata, 'database', vdb)
else: v_germ = os.path.join(igdata, 'database', 'imgt_%s_%s_v' % (organism, loci))
v_germ = _resolve_db(igdata, 'v', organism, loci, explicit=vdb)
if v_germ is None:
printError('No V database found for organism "%s" and loci "%s" with "airrc-imgt" or "imgt" prefix. '
'Specify --vdb, --ddb and --jdb explicitly.' % (organism, loci))
# Set D database
if ddb is not None: d_germ = os.path.join(igdata, 'database', ddb)
else: d_germ = os.path.join(igdata, 'database', 'imgt_%s_%s_d' % (organism, loci))
d_germ = _resolve_db(igdata, 'd', organism, loci, explicit=ddb)
if d_germ is None:
printError('No D database found for organism "%s" and loci "%s" with "airrc-imgt" or "imgt" prefix. '
'Specify --vdb, --ddb and --jdb explicitly.' % (organism, loci))
# Set J database
if jdb is not None: j_germ = os.path.join(igdata, 'database', jdb)
else: j_germ = os.path.join(igdata, 'database', 'imgt_%s_%s_j' % (organism, loci))
# Set C database
if cdb is not None: c_germ = os.path.join(igdata, 'database', cdb)
else: c_germ = os.path.join(igdata, 'database', 'imgt_%s_%s_c' % (organism, loci))
j_germ = _resolve_db(igdata, 'j', organism, loci, explicit=jdb)
if j_germ is None:
printError('No J database found for organism "%s" and loci "%s" with "airrc-imgt" or "imgt" prefix. '
'Specify --vdb, --ddb and --jdb explicitly.' % (organism, loci))
# Set C database (optional; warn if not found rather than error)
c_germ = _resolve_db(igdata, 'c', organism, loci, explicit=cdb)
if c_germ is None:
printWarning('No C database found for organism "%s" and loci "%s" with "airrc-imgt" or "imgt" prefix. '
'Specify --cdb explicitly if C-region annotation is required.' % (organism, loci))
c_germ = os.path.join(igdata, 'database', 'imgt_%s_%s_c' % (organism, loci))

# Define IgBLAST command
cmd = [exec,
Expand Down Expand Up @@ -234,8 +276,10 @@ def runIgBLASTP(fasta, igdata, loci='ig', organism='human', vdb=None, output=Non
printError('Invalid receptor type %s.' % loci)

# Set V database
if vdb is not None: v_germ = os.path.join(igdata, 'database', vdb)
else: v_germ = os.path.join(igdata, 'database', 'imgt_aa_%s_%s_v' % (organism, loci))
v_germ = _resolve_db(igdata, 'v', organism, loci, explicit=vdb, aa=True)
if v_germ is None:
printError('No V database found for organism "%s" and loci "%s" with "airrc-imgt_aa" or "imgt_aa" prefix. '
'Specify --vdb explicitly.' % (organism, loci))

# Define IgBLAST command
cmd = [exec,
Expand Down
Loading