Mercurial > repos > cpt > cpt_get_orfs

annotate get_orfs_or_cdss.py @ 6:f56389d8abda draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:52:07 +0000
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1 #!/usr/bin/env python
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2 import argparse
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3 import logging
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4 from cpt import OrfFinder
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6 logging.basicConfig()
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7 log = logging.getLogger()
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8
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9
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10 if __name__ == "__main__":
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11 parser = argparse.ArgumentParser(description="Get open reading frames")
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12 parser.add_argument("fasta_file", type=argparse.FileType("r"), help="Fasta file")
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13
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14 parser.add_argument(
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15 "-f",
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16 "--format",
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17 dest="seq_format",
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18 default="fasta",
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19 help="Sequence format (e.g. fasta, fastq, sff)",
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20 )
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21 parser.add_argument(
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22 "--table", dest="table", default=1, help="NCBI Translation table", type=int
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23 )
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24 parser.add_argument(
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25 "-t",
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26 "--ftype",
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27 dest="ftype",
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28 choices=("CDS", "ORF"),
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29 default="ORF",
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30 help="Find ORF or CDSs",
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31 )
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32 parser.add_argument(
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33 "-e",
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34 "--ends",
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35 dest="ends",
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36 choices=("open", "closed"),
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37 default="closed",
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38 help="Open or closed. Closed ensures start/stop codons are present",
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39 )
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40 parser.add_argument(
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41 "-m",
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42 "--mode",
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43 dest="mode",
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44 choices=("all", "top", "one"),
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45 default="all",
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46 help="Output all ORFs/CDSs from sequence, all ORFs/CDSs "
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47 "with max length, or first with maximum length",
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48 )
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49 parser.add_argument(
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50 "--min_len", dest="min_len", default=10, help="Minimum ORF/CDS length", type=int
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51 )
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52 parser.add_argument(
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53 "--strand",
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54 dest="strand",
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55 choices=("both", "forward", "reverse"),
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56 default="both",
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57 help="select strand",
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58 )
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59
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60 parser.add_argument(
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61 "--on",
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62 dest="out_nuc",
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63 type=argparse.FileType("w"),
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64 default="out.fna",
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65 help="Output nucleotide sequences",
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66 )
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67 parser.add_argument(
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68 "--op",
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69 dest="out_prot",
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70 type=argparse.FileType("w"),
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71 default="out.fa",
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72 help="Output protein sequences",
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73 )
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74 parser.add_argument(
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75 "--ob",
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76 dest="out_bed",
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77 type=argparse.FileType("w"),
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78 default="out.bed",
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79 help="Output BED file",
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80 )
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81 parser.add_argument(
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82 "--og",
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83 dest="out_gff3",
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84 type=argparse.FileType("w"),
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85 default="out.gff3",
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86 help="Output GFF3 file",
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87 )
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88 parser.add_argument("-v", action="version", version="0.3.0")
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89 args = parser.parse_args()
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90
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91 of = OrfFinder(args.table, args.ftype, args.ends, args.min_len, args.strand)
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92 of.locate(args.fasta_file, args.out_nuc, args.out_prot, args.out_bed, args.out_gff3)