input_other_top_gff = "%s.other_top.target.gff" % args.input_prefix
input_other_secondary_gff = "%s.other_secondary.target.gff" % args.input_prefix
precise_top_hints = "%s.precise_top.target.hints.gff" % args.output_prefix
precise_secondary_hints = "%s.precise_secondary.target.hints.gff" % args.output_prefix
other_top_hints = "%s.other_top.target.hints.gff" % args.output_prefix
other_secondary_hints = "%s.other_secondary.target.hints.gff" % args.output_prefix
AUGUSTUS.path = args.augustus_script_dir
AUGUSTUS.exonerate_to_hints(input_precise_top_gff,
precise_top_hints,
priority=args.full_top_hits_priority,
min_intron_len=args.min_intron_len,
max_intron_len=args.max_intron_len,
CDS_part_cutoff=args.full_top_hits_CDS_part_cutoff,
source=args.source_for_full_top_hits,
with_utrs=args.include_utr_hints)
AUGUSTUS.exonerate_to_hints(
input_precise_secondary_gff,
precise_secondary_hints,
priority=args.full_secondary_hits_priority,
min_intron_len=args.min_intron_len,
max_intron_len=args.max_intron_len,
CDS_part_cutoff=args.full_secondary_hits_CDS_part_cutoff,
source=args.source_for_full_secondary_hits,
with_utrs=args.include_utr_hints)
AUGUSTUS.exonerate_to_hints(
secondary_hits_gff = "%s.target.secondary_hits.gff" % args.output_prefix
top_hits_gff_hints = "%s.target.top_hits.hints.gff" % args.output_prefix
secondary_hits_gff_hints = "%s.target.secondary_hits.hints.gff" % args.output_prefix
Exonerate.extract_top_hits_from_target_gff(
args.input,
top_hits_gff,
secondary_hits_gff,
id_white_list_file=args.white_id_file,
max_hits_per_query=args.max_hits_per_query)
AUGUSTUS.path = args.augustus_script_dir
AUGUSTUS.exonerate_to_hints(top_hits_gff,
top_hits_gff_hints,
priority=args.top_hits_priority,
min_intron_len=args.min_intron_len,
max_intron_len=args.max_intron_len,
CDS_part_cutoff=args.top_hits_CDS_part_cutoff,
source=args.source_for_top_hits,
with_utrs=args.include_utr_hints)
AUGUSTUS.exonerate_to_hints(
secondary_hits_gff,
secondary_hits_gff_hints,
priority=args.secondary_hits_priority,
min_intron_len=args.min_intron_len,
max_intron_len=args.max_intron_len,
CDS_part_cutoff=args.secondary_hits_CDS_part_cutoff,
source=args.source_for_secondary_hits,
with_utrs=args.include_utr_hints)
