Mercurial > repos > cpt > cpt_fasta_translate
annotate fasta_translate.py @ 2:19b4f1a91dee draft default tip
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author | cpt |
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date | Fri, 05 Jan 2024 05:51:00 +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 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)) |