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1 #!/usr/bin/env python
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2 import sys
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3 import logging
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4 import argparse
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5 from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature
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6 #from Bio.SeqFeature import SeqFeature
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7 from gff3 import feature_lambda, feature_test_type
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8
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9 logging.basicConfig(level=logging.INFO)
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10 log = logging.getLogger(__name__)
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11
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12
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13 def fixed_feature(rec):
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14 for feature in feature_lambda(
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15 rec.features, feature_test_type, {"type": "CDS"}, subfeatures=True
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16 ):
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17 import random
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18
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19 fid = feature.qualifiers["ID"][0] + "_" + str(random.random())
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20 gene = gffSeqFeature(
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21 location=feature.location,
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22 type="gene",
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23 qualifiers={"ID": [fid], "source": ["cpt.fixModel"]},
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24 )
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25 # Below that we have an mRNA
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26 mRNA = gffSeqFeature(
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27 location=feature.location,
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28 type="mRNA",
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29 qualifiers={"source": ["cpt.fixModel"], "ID": ["%s.mRNA" % fid], "Parent": gene.qualifiers["ID"]},
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30 )
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31 feature.qualifiers["ID"] = [fid + ".CDS"]
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32 feature.qualifiers["Parent"] = mRNA.qualifiers["ID"]
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33
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34 mRNA.sub_features = [feature]
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35 gene.sub_features = [mRNA]
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36 yield gene
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37
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38
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39 def gff_filter(gff3):
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40 for rec in gffParse(gff3):
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41 rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start)
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42 rec.annotations = {}
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43 gffWrite([rec], sys.stdout)
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44
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45
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46 if __name__ == "__main__":
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47 parser = argparse.ArgumentParser(description="add parent gene features to CDSs")
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48 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
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49 args = parser.parse_args()
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50 gff_filter(**vars(args))
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