SequenceRoutines.extract_sequence_by_ids(
output_pep, output_swissprot_pfam_and_hints_supported_transcripts_ids,
output_swissprot_pfam_and_hints_supported_transcripts_pep)
print("Extracting evidence...")
AUGUSTUS.extract_evidence_by_ids(
output_evidence_stats,
output_swissprot_pfam_or_hints_supported_transcripts_ids,
output_swissprot_pfam_or_hints_supported_transcripts_evidence)
AUGUSTUS.extract_evidence_by_ids(
output_evidence_stats,
output_swissprot_pfam_and_hints_supported_transcripts_ids,
output_swissprot_pfam_and_hints_supported_transcripts_evidence)
print("Extracting longest isoforms...")
AUGUSTUS.extract_longest_isoforms(
output_swissprot_pfam_or_hints_supported_transcripts_evidence,
output_swissprot_pfam_or_hints_supported_transcripts_longest_pep_evidence
)
AUGUSTUS.extract_longest_isoforms(
output_swissprot_pfam_and_hints_supported_transcripts_evidence,
output_swissprot_pfam_and_hints_supported_transcripts_longest_pep_evidence
)
print("Extracting evidence...")
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)
import argparse
from RouToolPa.Tools.Annotation import AUGUSTUS
parser = argparse.ArgumentParser()
parser.add_argument("-i",
"--input",
action="store",
dest="input",
required=True,
help="Input evidence file")
parser.add_argument("-o",
"--output",
action="store",
dest="output",
required=True,
help="File to write filtered evidence file")
parser.add_argument("-m",
"--min_fraction",
action="store",
dest="min_fraction",
default=0,
type=float,
help="Minimum fraction of transcript supported by hints")
args = parser.parse_args()
AUGUSTUS.extract_longest_isoforms(args.input,
args.output,
minimum_supported_fraction=args.min_fraction)