def merge_gffs(rna_gff_files, cds_gff_files, contigs_fasta_file,
output_file_prefix):
# parse RNA GFF files
rna_hits = {f: get_gff_hits(f) for f in rna_gff_files}
# parse CDS files
cds_hits = {}
for cds_gff_file in cds_gff_files:
for contig, hits in generate_hits(cds_gff_file,
format=GFF,
sort='score'):
# get regions with rRNAs for this contig
rna_regions = get_rna_regions(rna_hits, contig)
# collect CDSs that don't overlap
cds_hits.setdefault(contig, []).extend(
[h for h in hits if h.checkForOverlap(rna_regions)[1] is None])
# the source data
hit_list_dicts = list(rna_hits.values())
hit_list_dicts.append(cds_hits)
# output files
with open(output_file_prefix + ".gff", 'w') as GFFOUT:
with open(output_file_prefix + ".fna", 'w') as FNAOUT:
with open(output_file_prefix + ".faa", 'w') as FAAOUT:
write_annotations_to_files(hit_list_dicts,
contigs_fasta_file,
GFFOUT,
FNAOUT,
FAAOUT)
def get_gff_hits(hit_table_gff, **filter_args):
filter_args.setdefault('sort', 'score')
filter_args.setdefault('nonoverlapping', True)
return {
c: list(h)
for c, h in generate_hits(hit_table_gff, format=GFF, **filter_args)
}
def merge_gffs(rna_gff_files, cds_gff_files, contigs_fasta_file,
output_file_prefix):
# parse RNA GFF files
rna_hits = {f: get_gff_hits(f) for f in rna_gff_files}
# parse CDS files
cds_hits = {}
for cds_gff_file in cds_gff_files:
for contig, hits in generate_hits(cds_gff_file,
format=GFF,
sort='score'):
# get regions with rRNAs for this contig
rna_regions = get_rna_regions(rna_hits, contig)
# collect CDSs that don't overlap
cds_hits.setdefault(contig, []).extend(
[h for h in hits if h.checkForOverlap(rna_regions)[1] is None])
# the source data
hit_list_dicts = list(rna_hits.values())
hit_list_dicts.append(cds_hits)
# output files
with open(output_file_prefix + ".gff", 'w') as GFFOUT:
with open(output_file_prefix + ".fna", 'w') as FNAOUT:
with open(output_file_prefix + ".faa", 'w') as FAAOUT:
write_annotations_to_files(hit_list_dicts,
contigs_fasta_file,
GFFOUT,
FNAOUT,
FAAOUT)
def get_gff_hits(hit_table_gff, **filter_args):
filter_args.setdefault('sort', 'score')
filter_args.setdefault('nonoverlapping', True)
return {c: list(h) for c, h in generate_hits(hit_table_gff,
format=GFF,
**filter_args)}
def get_gff_hits(hit_table_gff, **filter_args):
return {c: list(h) for c, h in generate_hits(hit_table_gff, format=GFF, **filter_args)}
