output_swissprot_pfam_supported_transcripts_ids,
output_supported_stats_ids,
output_swissprot_pfam_and_hints_supported_transcripts_ids,
mode="common")
print("Extracting sequences...")
SequenceRoutines.extract_sequence_by_ids(
output_pep, output_swissprot_pfam_or_hints_supported_transcripts_ids,
output_swissprot_pfam_or_hints_supported_transcripts_pep)
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...")
parser.add_argument("-i",
"--input",
action="store",
dest="input",
required=True,
help="Input file with AUGUSTUS evidence")
parser.add_argument("-o",
"--output",
action="store",
dest="output",
required=True,
help="Output file")
parser.add_argument("-d",
"--id_file",
action="store",
dest="id_file",
required=True,
help="File with ids to extract")
parser.add_argument("-m",
"--mode",
action="store",
dest="mode",
default="transcript",
help="Prefix of output files. Default - transcript")
args = parser.parse_args()
AUGUSTUS.extract_evidence_by_ids(args.input,
args.id_file,
args.output,
mode=args.mode)