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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:57:00 +0000
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1 #!/usr/bin/env python
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2 import sys
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3 import argparse
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4 import logging
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5 from Bio import SeqIO
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6 from CPT_GFFParser import gffParse, gffWrite
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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 require_shinefind(gff3, fasta):
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14 # Load up sequence(s) for GFF3 data
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15 seq_dict = SeqIO.to_dict(SeqIO.parse(fasta, "fasta"))
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16 # Parse GFF3 records
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17 for record in gffParse(gff3, base_dict=seq_dict):
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18 # Reopen
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19 genes = list(
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20 feature_lambda(
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21 record.features, feature_test_type, {"type": "gene"}, subfeatures=True
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22 )
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23 )
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24 good_genes = []
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25 for gene in genes:
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26 cdss = list(
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27 feature_lambda(
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28 gene.sub_features,
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29 feature_test_type,
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30 {"type": "CDS"},
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31 subfeatures=False,
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32 )
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33 )
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34 if len(cdss) == 0:
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35 continue
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36
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37 one_good_cds = False
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38 for cds in cdss:
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39 if cds.extract(record).seq[0:3].upper() in ("GTG", "ATG", "TTG"):
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40 one_good_cds = True
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41
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42 if one_good_cds:
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43 good_genes.append(gene)
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44 record.features = good_genes
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45 record.annotations = {}
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46 yield record
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47
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48
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49 if __name__ == "__main__":
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50 parser = argparse.ArgumentParser(description="Require specific start codons")
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51 parser.add_argument("fasta", type=argparse.FileType("r"), help="Fasta Genome")
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52 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
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53 args = parser.parse_args()
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54
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55 for rec in require_shinefind(**vars(args)):
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56 gffWrite([rec], sys.stdout)