Mercurial > repos > bgruening > augustus

annotate extract_features.py @ 17:de5f42e9a85c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 69d542836dbce9261906bb0d1e7ef39f9712f4a3
author iuc
date Sun, 15 Dec 2024 09:09:35 +0000
parents 66c8e9d8d1c4
children
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1
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1 #!/usr/bin/env python
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2
10
cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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3 import argparse
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4 import sys
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5 import textwrap
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6
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cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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7
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8 def main(args):
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9 """
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10 Extract the protein and coding section from an augustus gff, gtf file
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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11 Example file:
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12 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
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13 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
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14 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
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15 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
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16 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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17 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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18 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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19 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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20 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
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21 # end gene g1
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22 ###
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23 #
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24 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
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25 #
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26 # Predicted genes for sequence number 2 on both strands
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27 # start gene g2
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28 HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2
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29 HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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30 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1
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31 HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1
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32 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1
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33 """
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34 protein_seq = ""
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35 coding_seq = ""
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36 if args.protein:
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37 po = open(args.protein, "w+")
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38 if args.codingseq:
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39 co = open(args.codingseq, "w+")
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40
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41 for line in sys.stdin:
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42 # protein- and coding-sequence are stored as comments
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43 if line.startswith("#"):
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44 line = line[2:].strip()
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45 if line.startswith("start gene"):
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46 gene_name = line[11:].strip()
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47
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48 if protein_seq:
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49 if line.endswith("]"):
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50 protein_seq += line[:-1]
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51 po.write(
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52 ">%s\n%s\n"
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53 % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
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54 )
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55 protein_seq = ""
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56 else:
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57 protein_seq += line
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cb47e789ccaa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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59 if coding_seq:
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60 if line.endswith("]"):
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61 coding_seq += line[:-1]
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62 co.write(
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63 ">%s\n%s\n"
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64 % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
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65 )
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66 coding_seq = ""
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67 else:
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68 coding_seq += line
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69
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70 if args.protein and line.startswith("protein sequence = ["):
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71 if line.endswith("]"):
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72 protein_seq = line[20:-1]
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73 po.write(
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74 ">%s\n%s\n"
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75 % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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76 )
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77 protein_seq = ""
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78 else:
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79 line = line[20:]
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80 protein_seq = line
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81
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82 if args.codingseq and line.startswith("coding sequence = ["):
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83 if line.endswith("]"):
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84 coding_seq = line[19:-1]
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85 co.write(
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86 ">%s\n%s\n"
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87 % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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88 )
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89 coding_seq = ""
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90 else:
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91 line = line[19:]
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92 coding_seq = line
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93
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94 if args.codingseq:
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95 co.close()
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96 if args.protein:
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97 po.close()
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98
10
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100 if __name__ == "__main__":
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101 parser = argparse.ArgumentParser()
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102 parser.add_argument("-p", "--protein", help="Path to the protein file.")
66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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103 parser.add_argument("-c", "--codingseq", help="Path to the coding file.")
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105 args = parser.parse_args()
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66c8e9d8d1c4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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106 main(args)