Mercurial > repos > cpt > cpt_fix_sixpack

annotate gff3_fix_sixpack.py @ 3:efa4dfc23549 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:42:28 +0000
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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
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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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13 def fixed_feature(rec):
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14 # Get all gene features to remove the mRNAs from
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15 for feature in feature_lambda(
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16 rec.features, feature_test_type, {"type": "gene"}, subfeatures=True
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17 ):
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18 gene = feature
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19 sub_features = []
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20 # Filter out mRNA subfeatures, save other ones to new gene object.
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21 for sf in feature_lambda(
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22 feature.sub_features,
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23 feature_test_type,
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24 {"type": "mRNA"},
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25 subfeatures=True,
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26 invert=True,
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27 ):
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28 sf.qualifiers["Parent"] = gene.qualifiers["ID"]
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29 sub_features.append(sf)
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30 # override original subfeatures with our filtered list
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31 gene.sub_features = sub_features
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32 yield gene
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33
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34
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35 def gff_filter(gff3):
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36 for rec in gffParse(gff3):
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37 rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start)
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38 rec.annotations = {}
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39 gffWrite([rec], sys.stdout)
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40
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41
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42 if __name__ == "__main__":
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43 parser = argparse.ArgumentParser(description="Fix gene model from naive ORF caller")
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44 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
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45 args = parser.parse_args()
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46 gff_filter(**vars(args))