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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 Bio import SeqIO
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6 from Bio.Data import CodonTable
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7
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8 logging.basicConfig(level=logging.INFO)
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9 log = logging.getLogger()
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10
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11
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12 def translate(fasta_file, target="protein", table=11, strip_stops=False, met=False):
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13 records = list(SeqIO.parse(fasta_file, "fasta"))
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14
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15 for record in records:
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16 if target == "protein":
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17 mod = len(record.seq) % 3
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18 if mod != 0:
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19 record.seq = record.seq[0:-mod]
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20
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21 # Read http://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html#transcribe
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22 # for valid CDS conditions.
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23
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24 # Will first try to translate sequence as a CDS,
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25 # then just as a sequence if this fails.
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26
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27 try:
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28 tmpseq = record.seq.translate(table=table, cds=True)
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29 except CodonTable.TranslationError as cte:
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30 log.info("Translation issue at %s: %s", record.id, cte)
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31 tmpseq = record.seq.translate(table=table, cds=False)
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32
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33 # check if stop in middle of protein
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34 if "*" in tmpseq:
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35 log.info(
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36 "Trimming %s from %s to %s due to stop codons",
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37 record.id,
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38 len(record.seq),
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39 3 * len(tmpseq) - 3,
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40 )
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41 tmpseq = tmpseq[0 : str(tmpseq).index("*")]
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42
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43 # add stop to end if strip_stops=False
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44 if not strip_stops:
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45 tmpseq = tmpseq + "*"
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46
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47 if met:
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48 tmpseq = "M" + tmpseq[1:]
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49
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50 record.seq = tmpseq
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51 if len(record.seq) > 0:
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52 SeqIO.write(record, sys.stdout, "fasta")
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53 else:
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54 record.seq = record.seq.transcribe()
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55 SeqIO.write(record, sys.stdout, "fasta")
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56
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57
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58 if __name__ == "__main__":
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59 parser = argparse.ArgumentParser(description="Translate fasta file")
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60 parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Fasta file")
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61 parser.add_argument("--target", choices=["protein", "rna"])
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62 parser.add_argument(
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63 "--table",
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64 type=int,
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65 default=11,
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66 help="Translation table to use",
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67 choices=range(1, 23),
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68 )
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69 parser.add_argument(
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70 "--strip_stops", action="store_true", help="Remove stop characters"
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71 )
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72 parser.add_argument(
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73 "--met", action="store_true", help="Convert first residue to Met"
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74 )
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75
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76 args = parser.parse_args()
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77 translate(**vars(args))
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