def annotate_hits_file(seed_orthologs_file, annot_file, hmm_hits_file, args):
HIT_HEADER = [
"#query_name",
"seed_eggNOG_ortholog",
"seed_ortholog_evalue",
"seed_ortholog_score",
"best_tax_level",
]
HIT_OG_HEADER = [
"taxonomic scope", "eggNOG OGs", "best eggNOG OG",
"COG Functional cat.", "eggNOG free text desc."
]
start_time = time.time()
seq2bestOG = {}
if pexists(hmm_hits_file):
seq2bestOG = get_seq_hmm_matches(hmm_hits_file)
seq2annotOG = annota.get_ogs_annotations(
set([v[0] for v in seq2bestOG.itervalues()]))
print colorify("Functional annotation of refined hits starts now", 'green')
OUT = open(annot_file, "w")
if args.report_orthologs:
ORTHOLOGS = open(annot_file + ".orthologs", "w")
if not args.no_file_comments:
print >> OUT, '# emapper version:', get_version(
), 'emapper DB:', get_db_version()
print >> OUT, '# command: ./emapper.py ', ' '.join(sys.argv[1:])
print >> OUT, '# time: ' + time.ctime()
print >> OUT, '\t'.join(HIT_HEADER + ANNOTATIONS_HEADER +
HIT_OG_HEADER)
qn = 0
pool = multiprocessing.Pool(args.cpu)
for result in pool.imap(annotate_hit_line,
iter_hit_lines(seed_orthologs_file, args)):
qn += 1
if qn and (qn % 500 == 0):
total_time = time.time() - start_time
print >> sys.stderr, qn, total_time, "%0.2f q/s (func. annotation)" % (
(float(qn) / total_time))
sys.stderr.flush()
if result:
(query_name, best_hit_name, best_hit_evalue, best_hit_score,
annotations, annot_level_max, swallowest_level, match_nogs,
orthologs) = result
if query_name in seq2bestOG:
(hitname, evalue, score, qlength, hmmfrom, hmmto, seqfrom,
seqto, q_coverage) = seq2bestOG[query_name]
bestOG = '%s|%s|%s' % (hitname, evalue, score)
og_cat, og_desc = seq2annotOG.get(hitname, ['', ''])
else:
bestOG = 'NA|NA|NA'
og_cat, og_desc = annota.get_best_og_description(match_nogs)
if args.report_orthologs:
print >> ORTHOLOGS, '\t'.join(
map(str, (query_name, ','.join(orthologs))))
# prepare annotations for printing
annot_columns = [
query_name, best_hit_name,
str(best_hit_evalue),
str(best_hit_score), LEVEL_NAMES[swallowest_level]
]
for h in ANNOTATIONS_HEADER:
if h in annotations:
annot_columns.append(','.join(sorted(annotations[h])))
else:
annot_columns.append('')
annot_columns.extend([
annot_level_max, ','.join(match_nogs), bestOG,
og_cat.replace('\n', ''),
og_desc.replace('\n', ' ')
])
print >> OUT, '\t'.join(annot_columns)
#OUT.flush()
pool.terminate()
elapsed_time = time.time() - start_time
if not args.no_file_comments:
print >> OUT, '# %d queries scanned' % (qn)
print >> OUT, '# Total time (seconds):', elapsed_time
print >> OUT, '# Rate:', "%0.2f q/s" % ((float(qn) / elapsed_time))
OUT.close()
if args.report_orthologs:
ORTHOLOGS.close()
print colorify(" Processed queries:%s total_time:%s rate:%s" %\
(qn, elapsed_time, "%0.2f q/s" % ((float(qn) / elapsed_time))), 'lblue')
def annotate_hits_file(seed_orthologs_file, annot_file, hmm_hits_file, args):
annot_header = (
"#query_name",
"seed_eggNOG_ortholog",
"seed_ortholog_evalue",
"seed_ortholog_score",
"predicted_gene_name",
"GO_terms",
"KEGG_KOs",
"BiGG_reactions",
"Annotation_tax_scope",
"OGs",
"bestOG|evalue|score",
"COG cat",
"eggNOG annot",
)
start_time = time.time()
seq2bestOG = {}
if pexists(hmm_hits_file):
seq2bestOG = get_seq_hmm_matches(hmm_hits_file)
seq2annotOG = annota.get_ogs_annotations(
set([v[0] for v in seq2bestOG.itervalues()]))
print colorify("Functional annotation of refined hits starts now", 'green')
OUT = open(annot_file, "w")
if args.report_orthologs:
ORTHOLOGS = open(annot_file + ".orthologs", "w")
if not args.no_file_comments:
print >> OUT, '# emapper version:', get_version(
), 'emapper DB:', get_db_version()
print >> OUT, '# command: ./emapper.py ', ' '.join(sys.argv[1:])
print >> OUT, '# time: ' + time.ctime()
print >> OUT, '\t'.join(annot_header)
qn = 0
pool = multiprocessing.Pool(args.cpu)
for result in pool.imap(annotate_hit_line,
iter_hit_lines(seed_orthologs_file, args)):
qn += 1
if qn and (qn % 500 == 0):
total_time = time.time() - start_time
print >> sys.stderr, qn, total_time, "%0.2f q/s (refinement)" % (
(float(qn) / total_time))
sys.stderr.flush()
if result:
(query_name, best_hit_name, best_hit_evalue, best_hit_score,
best_name, gos, kegg, bigg, annot_level_max, match_nogs,
orthologs) = result
if query_name in seq2bestOG:
(hitname, evalue, score, qlength, hmmfrom, hmmto, seqfrom,
seqto, q_coverage) = seq2bestOG[query_name]
bestOG = '%s|%s|%s' % (hitname, evalue, score)
og_cat, og_desc = seq2annotOG.get(hitname, ['', ''])
else:
bestOG = 'NA|NA|NA'
og_cat, og_desc = annota.get_best_og_description(match_nogs)
if args.report_orthologs:
print >> ORTHOLOGS, '\t'.join(
map(str, (query_name, ','.join(orthologs))))
print >> OUT, '\t'.join(
map(str, (
query_name,
best_hit_name,
best_hit_evalue,
best_hit_score,
best_name,
','.join(sorted(gos)),
','.join(sorted(kegg)),
','.join(sorted(bigg)),
annot_level_max,
','.join(match_nogs),
bestOG,
og_cat.replace('\n', ''),
og_desc.replace('\n', ' '),
)))
OUT.flush()
pool.terminate()
elapsed_time = time.time() - start_time
if not args.no_file_comments:
print >> OUT, '# %d queries scanned' % (qn)
print >> OUT, '# Total time (seconds):', elapsed_time
print >> OUT, '# Rate:', "%0.2f q/s" % ((float(qn) / elapsed_time))
OUT.close()
if args.report_orthologs:
ORTHOLOGS.close()
print colorify(" Processed queries:%s total_time:%s rate:%s" %\
(qn, elapsed_time, "%0.2f q/s" % ((float(qn) / elapsed_time))), 'lblue')