#!/usr/bin/env python
__author__ = 'Sergei F. Kliver'
import argparse
from Routines import AnnotationsRoutines
parser = argparse.ArgumentParser()
parser.add_argument("-i",
"--input_gff",
action="store",
dest="input_gff",
help="Gff file with annotations to extract")
parser.add_argument("-o",
"--output_gff",
action="store",
dest="output_gff",
help="Output gff file with extracted transcripts")
parser.add_argument("-d",
"--ids_file",
action="store",
dest="ids_file",
help="File with ids of transcripts to extract")
args = parser.parse_args()
AnnotationsRoutines.extract_transcripts_by_ids(args.input_gff, args.ids_file,
args.output_gff)
SequenceRoutines.extract_sequence_by_ids(
output_pep, "%s.ids" %
output_swissprot_pfam_or_hints_supported_transcripts_longest_pep_evidence,
output_swissprot_pfam_or_hints_supported_transcripts_longest_pep)
SequenceRoutines.extract_sequence_by_ids(
output_pep, "%s.ids" %
output_swissprot_pfam_and_hints_supported_transcripts_longest_pep_evidence,
output_swissprot_pfam_and_hints_supported_transcripts_longest_pep)
for id_file in output_swissprot_pfam_or_hints_supported_transcripts_ids, \
output_swissprot_pfam_and_hints_supported_transcripts_ids, \
"%s.ids" % output_swissprot_pfam_or_hints_supported_transcripts_longest_pep_evidence, \
"%s.ids" % output_swissprot_pfam_and_hints_supported_transcripts_longest_pep_evidence:
out_pref = id_file[:-4]
out_gff = "%s.gff" % out_pref
AnnotationsRoutines.extract_transcripts_by_ids(output_gff, id_file,
out_gff)
for suffix in ".trimmed.cds", ".transcript":
SequenceRoutines.extract_sequence_by_ids(
"%s%s" % (args.output, suffix), id_file,
"%s%s" % (out_pref, suffix))
HMMER3.intersect_ids_from_files(
output_swissprot_pfam_or_hints_supported_transcripts_ids,
cds_with_inframe_stop_codons_ids,
output_swissprot_pfam_or_hints_supported_transcripts_inframe_stop_ids,
mode="common")
HMMER3.intersect_ids_from_files(
output_swissprot_pfam_and_hints_supported_transcripts_ids,
cds_with_inframe_stop_codons_ids,
output_swissprot_pfam_and_hints_supported_transcripts_inframe_stop_ids,