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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 idx, feature in enumerate(
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15 feature_lambda(
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16 rec.features, feature_test_type, {"types": ["tRNA", "tmRNA"]}, subfeatures=True
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17 )
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18 ):
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19
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20 fid = "%s-%03d" % (feature.type, 1 + idx)
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21 try:
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22 name = [feature.type + "-" + feature.qualifiers["Codon"][0]]
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23 except KeyError:
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24 name = [feature.qualifiers['product'][0]]
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25 try:
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26 origSource = feature.qualifiers["source"][0]
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27 except:
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28 origSource = "."
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29 gene = gffSeqFeature(
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30 location=feature.location,
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31 type="gene",
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32 qualifiers={"ID": [fid + ".gene"], "source": [origSource], "Name": name},
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33 )
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34 feature.qualifiers["Name"] = name
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35 # Below that we have an mRNA
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36 exon = gffSeqFeature(
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37 location=feature.location,
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38 type="exon",
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39 qualifiers={"source": [origSource], "ID": ["%s.exon" % fid], "Name": name},
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40 )
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41 feature.qualifiers["ID"] = [fid]
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42 exon.qualifiers["Parent"] = [fid]
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43 feature.qualifiers["Parent"] = [fid + ".gene"]
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44 # gene -> trna -> exon
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45 feature.sub_features = [exon]
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46 gene.sub_features = [feature]
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47 yield gene
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48
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49
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50 def gff_filter(gff3):
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51 found_gff = False
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52 for rec in gffParse(gff3):
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53 found_gff = True
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54 rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start)
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55 rec.annotations = {}
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56 gffWrite([rec], sys.stdout)
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57 if not found_gff:
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58 print("##gff-version 3")
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59
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60
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61 if __name__ == "__main__":
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62 parser = argparse.ArgumentParser(description="add parent gene features to CDSs")
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63 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
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64 args = parser.parse_args()
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65 gff_filter(**vars(args))
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