def correct_regions_from_gff(
self,
reference,
variants_vcf,
gff_file,
output_prefix=None,
feature_type_list=["CDS"],
unification_key="Parent",
#raw_seq_per_line=False,
vcf_with_masking=None,
override_vcf_by_mask=None,
use_ambiguous_nuccleotides=None):
feature_dict = AnnotationsRoutines.get_feature_dict(
gff_file,
output_prefix=output_prefix,
feature_type_list=feature_type_list,
unification_key=unification_key)
region_file = "%s.coordinates_only.list" % output_prefix
raw_regions = "%s.raw.seq" % output_prefix
final_regions = "%s.fasta" % output_prefix
regions_with_frameshift_file = "%s.frameshifts.region.ids" % output_prefix
self.correct_reference(
reference,
raw_regions,
variants_vcf,
raw_seq_per_line=True,
vcf_with_masking=vcf_with_masking,
override_vcf_by_mask=override_vcf_by_mask,
use_ambiguous_nuccleotides=use_ambiguous_nuccleotides,
interval_list=region_file)
region_with_frameshift = SynDict()
def new_regions_generator():
with open(raw_regions, "r") as in_fd:
for region_id in feature_dict:
seq = ""
for i in range(0, len(feature_dict[region_id])):
seq_fragment = in_fd.readline().strip()
if ((int(feature_dict[region_id][i][2]) -
int(feature_dict[region_id][i][1]) + 1) -
len(seq_fragment)) % 3 != 0:
if region_id not in region_with_frameshift:
region_with_frameshift[region_id] = [i]
else:
region_with_frameshift[region_id].append(i)
seq += seq_fragment
yield SeqRecord(
seq=Seq(seq) if feature_dict[region_id][0][3] == "+"
else Seq(seq).reverse_complement(),
id=region_id,
description="")
SeqIO.write(new_regions_generator(), final_regions, format="fasta")
region_with_frameshift.write(regions_with_frameshift_file,
splited_values=True)
parser.add_argument("-o",
"--output_prefix",
action="store",
dest="output_prefix",
required=True,
help="Output .gff file")
parser.add_argument("-t",
"--feature_types",
action="store",
dest="feature_types",
type=lambda s: s.split(","),
default=["CDS"],
help="Comma-separated list of feature types to extract. "
"Default: CDS only")
parser.add_argument(
"-u",
"--unification_key",
action="store",
dest="unification_key",
default="Parent",
help="Annotation entry to use for unification. Default: Parent")
args = parser.parse_args()
AnnotationsRoutines.get_feature_dict(args.input_gff,
output_prefix=args.output_prefix,
feature_type_list=args.feature_types,
unification_key=args.unification_key)