def main():
parser = argparse.ArgumentParser( description='Script for reporting of possible polycistronic genes transcripts based on a reference annotation and RNA-seq transcript assemblies')
## output file to be written
parser.add_argument('-r', '--reference_file', type=str, required=True, help='GFF3 file of a reference annotation' )
parser.add_argument('-q', '--query_file', type=str, required=True, help='GFF3 file with alternative annotation (such as an RNA-seq assemby)' )
parser.add_argument('-o', '--output_file', type=str, required=True, help='Path to an output file to be created' )
args = parser.parse_args()
(ref_assemblies, ref_feats) = biocodegff.get_gff3_features(args.reference_file)
(qry_assemblies, qry_genes) = biocodegff.get_gff3_features(args.query_file)
for assembly_id in ref_assemblies:
# we expect to find this assembly ID in the qry set too
if assembly_id not in qry_assemblies:
print("WARN: expected to find assembly_id {0} in both reference and query sets".format(assembly_id))
continue
for ref_gene in ref_assemblies[assembly_id].genes():
overlaps = list()
polypeptides = ref_gene.polypeptides()
if len(polypeptides) == 0:
print("WARN: skipped gene {0} because it has no polypeptides".format(ref_gene.id))
continue
ref_annot = ref_gene.polypeptides()[0].annotation
for qry_gene in qry_assemblies[assembly_id].genes():
overlap = ref_gene.overlaps_with(qry_gene)
if overlap:
#print("DEBUG: {0} and {1} appear to overlap".format(ref_gene.id, qry_gene.id) )
overlaps.append(overlap)
# add a dbxref to the gene
ref_annot.add_dbxref("overlaps_old_locusTagID:{0}".format(qry_gene.id))
if len(overlaps) > 0:
print("INFO: ref_gene {0} had {1} overlaps".format(ref_gene.id, len(overlaps)))
biocodegff.print_gff3_from_assemblies(assemblies=ref_assemblies, ofh=open(args.output_file, 'w'))
def main():
parser = argparse.ArgumentParser(
description=
'Script for reporting of possible polycistronic genes transcripts based on a reference annotation and RNA-seq transcript assemblies'
)
## output file to be written
parser.add_argument('-r',
'--reference_file',
type=str,
required=True,
help='GFF3 file of a reference annotation')
parser.add_argument(
'-q',
'--query_file',
type=str,
required=True,
help=
'GFF3 file with alternative annotation (such as an RNA-seq assemby)')
parser.add_argument('-o',
'--output_file',
type=str,
required=True,
help='Path to an output file to be created')
args = parser.parse_args()
(ref_assemblies,
ref_feats) = biocodegff.get_gff3_features(args.reference_file)
(qry_assemblies, qry_genes) = biocodegff.get_gff3_features(args.query_file)
for assembly_id in ref_assemblies:
# we expect to find this assembly ID in the qry set too
if assembly_id not in qry_assemblies:
print(
"WARN: expected to find assembly_id {0} in both reference and query sets"
.format(assembly_id))
continue
for ref_gene in ref_assemblies[assembly_id].genes():
overlaps = list()
polypeptides = ref_gene.polypeptides()
if len(polypeptides) == 0:
print("WARN: skipped gene {0} because it has no polypeptides".
format(ref_gene.id))
continue
ref_annot = ref_gene.polypeptides()[0].annotation
for qry_gene in qry_assemblies[assembly_id].genes():
overlap = ref_gene.overlaps_with(qry_gene)
if overlap:
#print("DEBUG: {0} and {1} appear to overlap".format(ref_gene.id, qry_gene.id) )
overlaps.append(overlap)
# add a dbxref to the gene
ref_annot.add_dbxref("overlaps_old_locusTagID:{0}".format(
qry_gene.id))
if len(overlaps) > 0:
print("INFO: ref_gene {0} had {1} overlaps".format(
ref_gene.id, len(overlaps)))
biocodegff.print_gff3_from_assemblies(assemblies=ref_assemblies,
ofh=open(args.output_file, 'w'))
def main():
parser = argparse.ArgumentParser( description='Assigns functional annotation based on user-configurable evidence tiers')
## output file to be written
parser.add_argument('-c', '--config_file', type=str, required=True, help='Configuration file for annotation' )
parser.add_argument('-o', '--output_base', type=str, required=True, help='Base name/path of output files to be created' )
parser.add_argument('-f', '--output_format', type=str, required=False, default='gff3', help='Desired output format' )
args = parser.parse_args()
sources_log_fh = open("{0}.sources.log".format(args.output_base), 'wt')
configuration = yaml.load(open(args.config_file).read())
check_configuration(configuration, args)
evidence = parse_evidence_config(configuration)
default_product_name = configuration['general']['default_product_name']
# stores any active SQLite3 db connections
db_conn = dict()
# this is a dict of biothings.Polypeptide objects
polypeptides = initialize_polypeptides(sources_log_fh, configuration['input']['polypeptide_fasta'], default_product_name)
for label in configuration['order']:
if label not in evidence:
raise Exception("ERROR: There is a label '{0}' in the 'order' section of the conf file that isn't present in the 'evidence' section".format(label))
if evidence[label]['type'] == 'HMMer3_htab':
index_conn, ev_db_conn = get_or_create_db_connections(type_ev='hmm_ev', configuration=configuration,
evidence=evidence, label=label, db_conn=db_conn, output_base=args.output_base)
index_conn.isolation_level = None
apply_hmm_evidence(polypeptides=polypeptides, ev_conn=ev_db_conn, config=configuration,
ev_config=evidence[label], label=label, index_conn=index_conn, log_fh=sources_log_fh)
elif evidence[label]['type'] == 'RAPSearch2_m8':
index_conn, ev_db_conn = get_or_create_db_connections(type_ev='blast_ev', configuration=configuration,
evidence=evidence, label=label, db_conn=db_conn, output_base=args.output_base)
index_conn.isolation_level = None
apply_blast_evidence(polypeptides=polypeptides, ev_conn=ev_db_conn, config=configuration,
ev_config=evidence[label], label=label, index_conn=index_conn, log_fh=sources_log_fh)
elif evidence[label]['type'] == 'TMHMM':
index_conn, ev_db_conn = get_or_create_db_connections(type_ev='tmhmm_ev', configuration=configuration,
evidence=evidence, label=label, db_conn=db_conn, output_base=args.output_base)
apply_tmhmm_evidence(polypeptides=polypeptides, ev_conn=ev_db_conn, config=configuration,
ev_config=evidence[label], label=label, log_fh=sources_log_fh)
elif evidence[label]['type'] == 'lipoprotein_motif_bsml':
index_conn, ev_db_conn = get_or_create_db_connections(type_ev='lipoprotein_motif_ev', configuration=configuration,
evidence=evidence, label=label, db_conn=db_conn, output_base=args.output_base)
apply_lipoprotein_motif_evidence(polypeptides=polypeptides, ev_conn=ev_db_conn, config=configuration,
ev_config=evidence[label], label=label, log_fh=sources_log_fh)
else:
raise Exception("ERROR: Unsupported evidence type '{0}' with label '{1}' in configuration file".format(evidence[label]['type'], label))
# close all db connections
for label in db_conn:
db_conn[label].close()
perform_final_checks(polypeptides=polypeptides, config=configuration, log_fh=sources_log_fh)
# Write the output
polyset = biothings.PolypeptideSet()
polyset.load_from_dict(polypeptides)
if args.output_format == 'fasta':
polyset.write_fasta(path="{0}.faa".format(args.output_base))
elif args.output_format == 'gff3':
## parse input GFF
(assemblies, ref_features) = biocodegff.get_gff3_features( configuration['input']['gff3'] )
## merge annotation with polypeptide collection
biocodegff.add_annotation(features=ref_features, polypeptide_set=polyset)
## print the new GFF
biocodegff.print_gff3_from_assemblies(assemblies=assemblies, ofh=open("{0}.gff3".format(args.output_base), 'wt'))
