Mercurial > repos > cpt > cpt_gff_add_parents
view cpt_gff_add_parent/gff3_add_parents_to_cds.py @ 0:60651e90119a draft
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author | cpt |
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date | Fri, 13 May 2022 04:54:17 +0000 |
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#!/usr/bin/env python import sys import logging import argparse from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature #from Bio.SeqFeature import SeqFeature from gff3 import feature_lambda, feature_test_type logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) def fixed_feature(rec): for feature in feature_lambda( rec.features, feature_test_type, {"type": "CDS"}, subfeatures=True ): import random fid = feature.qualifiers["ID"][0] + "_" + str(random.random()) gene = gffSeqFeature( location=feature.location, type="gene", qualifiers={"ID": [fid], "source": ["cpt.fixModel"]}, ) # Below that we have an mRNA mRNA = gffSeqFeature( location=feature.location, type="mRNA", qualifiers={"source": ["cpt.fixModel"], "ID": ["%s.mRNA" % fid], "Parent": gene.qualifiers["ID"]}, ) feature.qualifiers["ID"] = [fid + ".CDS"] feature.qualifiers["Parent"] = mRNA.qualifiers["ID"] mRNA.sub_features = [feature] gene.sub_features = [mRNA] yield gene def gff_filter(gff3): for rec in gffParse(gff3): rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start) rec.annotations = {} gffWrite([rec], sys.stdout) if __name__ == "__main__": parser = argparse.ArgumentParser(description="add parent gene features to CDSs") parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations") args = parser.parse_args() gff_filter(**vars(args))