def main(args):
# Output and intermediate files
hmm_hits_file = "%s.emapper.hmm_hits" % args.output
seed_orthologs_file = "%s.emapper.seed_orthologs" % args.output
annot_file = "%s.emapper.annotations" % args.output
orthologs_file = "%s.emapper.predict_orthologs" % args.output
if args.no_search:
output_files = [annot_file]
elif args.no_annot:
output_files = [hmm_hits_file, seed_orthologs_file]
else:
output_files = [hmm_hits_file, seed_orthologs_file, annot_file]
# convert to absolute path before changing directory
if args.annotate_hits_table:
args.annotate_hits_table = os.path.abspath(args.annotate_hits_table)
# force user to decide what to do with existing files
os.chdir(args.output_dir)
files_present = set([pexists(fname) for fname in output_files])
if True in files_present and not args.resume and not args.override:
print "Output files detected in disk. Use --resume or --override to continue"
raise emapperException()
if args.override:
for outf in output_files:
silent_rm(outf)
print '# ', get_version()
print '# ./emapper.py ', ' '.join(sys.argv[1:])
if args.scratch_dir:
# If resuming in and using --scratch_dir, transfer existing files.
if args.resume and args.scratch_dir:
for f in output_files:
if pexists(f):
print " Copying input file %s to scratch dir %s" % (
f, args.scratch_dir)
shutil.copy(f, args.scratch_dir)
# Change working dir
os.chdir(args.scratch_dir)
# Step 1. Sequence search
if not args.no_search:
if args.mode == 'diamond' and not args.no_search:
dump_diamond_matches(args.input, seed_orthologs_file, args)
elif args.mode == 'hmmer' and not args.no_search:
host, port, dbpath, scantype, idmap = setup_hmm_search(args)
# Start HMM SCANNING sequences (if requested)
if not pexists(hmm_hits_file) or args.override:
dump_hmm_matches(args.input, hmm_hits_file, dbpath, port,
scantype, idmap, args)
if not args.no_refine and (not pexists(seed_orthologs_file)
or args.override):
if args.db == 'viruses':
print 'Skipping seed ortholog detection in "viruses" database'
elif args.db in EGGNOG_DATABASES:
refine_matches(args.input, seed_orthologs_file,
hmm_hits_file, args)
else:
print 'refined hits not available for custom hmm databases.'
# Step 2. Annotation
if not args.no_annot:
annota.connect()
if args.annotate_hits_table:
if not os.path.exists(args.annotate_hits_table):
raise IOError(errno.ENOENT, os.strerror(errno.ENOENT),
args.annotate_hits_table)
annotate_hits_file(args.annotate_hits_table, annot_file,
hmm_hits_file, args)
elif args.db == 'viruses':
annotate_hmm_matches(hmm_hits_file, hmm_hits_file + '.annotations',
args)
OUT = open(annot_file, 'w')
for line in open(hmm_hits_file + '.annotations'):
if line.startswith('#') or not line.strip():
continue
(query, hitname, level, evalue, sum_score, query_length,
hmmfrom, hmmto, seqfrom, seqto, q_coverage, nm, desc,
cats) = line.split("\t")
if hitname != '-' and hitname != 'ERROR':
print >> OUT, '\t'.join(
map(str,
(query, hitname, evalue, sum_score, '', '', '',
'viruses', hitname + "@viruses", "%s|%s|%s" %
(hitname, evalue, sum_score),
cats.replace('\n', ''), desc.replace('\n', ' '))))
OUT.close()
else:
annotate_hits_file(seed_orthologs_file, annot_file, hmm_hits_file,
args)
if args.predict_ortho:
orthology.connect()
dump_orthologs(seed_orthologs_file, orthologs_file, args)
# If running in scratch, move files to real output dir and clean up
if args.scratch_dir:
for fname in output_files:
if pexists(fname):
print " Copying result file %s from scratch to %s" % (
fname, args.output_dir)
shutil.copy(annot_file, args.output_dir)
print " Cleaning result file %s from scratch dir" % (fname)
# Finalize and exit
print colorify('Done', 'green')
for f in output_files:
colorify('Result files:', 'yellow')
if pexists(f):
print " %s" % (f)
print 'Total time: %g secs' % (time.time() - _total_time)
if args.mode == 'hmmer':
print get_citation(['hmmer'])
elif args.mode == 'diamond':
print get_citation(['diamond'])
shutdown_server()
def main(args):
# Output and intermediate files
hmm_hits_file = "%s.emapper.hmm_hits" % args.output
seed_orthologs_file = "%s.emapper.seed_orthologs" % args.output
annot_file = "%s.emapper.annotations" % args.output
if args.no_search:
output_files = [annot_file]
elif args.no_annot:
output_files = [hmm_hits_file, seed_orthologs_file]
else:
output_files = [hmm_hits_file, seed_orthologs_file, annot_file]
# force user to decide what to do with existing files
os.chdir(args.output_dir)
files_present = set([pexists(fname) for fname in output_files])
if True in files_present and not args.resume and not args.override:
print "Output files detected in disk. Use --resume or --override to continue"
raise emapperException()
if args.override:
for outf in output_files:
silent_rm(outf)
print '# ', get_version()
print '# ./emapper.py ', ' '.join(sys.argv[1:])
if args.scratch_dir:
# If resuming in and using --scratch_dir, transfer existing files.
if args.resume and args.scratch_dir:
for f in output_files:
if pexists(f):
print " Copying input file %s to scratch dir %s" % (f, args.scratch_dir)
shutil.copy(f, args.scratch_dir)
# Change working dir
os.chdir(args.scratch_dir)
# Step 1. Sequence search
if not args.no_search:
if args.mode == 'diamond' and not args.no_search:
dump_diamond_matches(args.input, seed_orthologs_file, args)
elif args.mode == 'hmmer' and not args.no_search:
host, port, dbpath, scantype, idmap = setup_hmm_search(args)
# Start HMM SCANNING sequences (if requested)
if not pexists(hmm_hits_file) or args.override:
dump_hmm_matches(args.input, hmm_hits_file, dbpath, port, scantype, idmap, args)
if not args.no_refine and (not pexists(seed_orthologs_file) or args.override):
if args.db == 'viruses':
print 'Skipping seed ortholog detection in "viruses" database'
elif args.db in EGGNOG_DATABASES:
refine_matches(args.input, seed_orthologs_file, hmm_hits_file, args)
else:
print 'refined hits not available for custom hmm databases.'
# Step 2. Annotation
if not args.no_annot:
annota.connect()
if args.annotate_hits_table:
annotate_hits_file(args.annotate_hits_table, annot_file, hmm_hits_file, args)
elif args.db == 'viruses':
annotate_hmm_matches(hmm_hits_file, hmm_hits_file+'.annotations', args)
OUT = open(annot_file, 'w')
for line in open(hmm_hits_file+'.annotations'):
if line.startswith('#') or not line.strip():
continue
(query, hitname, level, evalue, sum_score, query_length,
hmmfrom, hmmto, seqfrom, seqto, q_coverage, nm, desc, cats) = line.split("\t")
if hitname != '-' and hitname != 'ERROR':
print >>OUT, '\t'.join(map(str, (query,
hitname,
evalue,
sum_score,
'',
'',
'',
'viruses',
hitname+"@viruses",
"%s|%s|%s" %(hitname, evalue, sum_score),
cats.replace('\n', ''),
desc.replace('\n', ' '))))
OUT.close()
else:
annotate_hits_file(seed_orthologs_file, annot_file, hmm_hits_file, args)
# If running in scratch, move files to real output dir and clean up
if args.scratch_dir:
for fname in output_files:
if pexists(fname):
print " Copying result file %s from scratch to %s" % (fname, args.output_dir)
shutil.copy(annot_file, args.output_dir)
print " Cleaning result file %s from scratch dir" %(fname)
# Finalize and exit
print colorify('Done', 'green')
for f in output_files:
colorify('Result files:', 'yellow')
if pexists(f):
print " %s" % (f)
print 'Total time: %g secs' % (time.time()-_total_time)
if args.mode == 'hmmer':
print get_citation(['hmmer'])
elif args.mode == 'diamond':
print get_citation(['diamond'])
shutdown_server()