Mercurial > repos > bgruening > augustus_training

annotate extract_features.py @ 1:1fbb1135da16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
author iuc
date Fri, 10 May 2019 08:52:20 -0400
parents 86c89c3bd99d
children 7be22100e5e1
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86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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1 #!/usr/bin/env python
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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2
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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3 import argparse
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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4 import sys
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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5 import textwrap
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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6
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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7
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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8 def main( args ):
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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9 """
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10 Extract the protein and coding section from an augustus gff, gtf file
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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11 Example file:
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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12 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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13 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
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14 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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15 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
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16 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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17 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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18 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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19 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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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
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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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
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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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 = ''
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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36 if args.protein:
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37 po = open( args.protein, 'w+' )
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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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:
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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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( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
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52 protein_seq = ''
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53 else:
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54 protein_seq += line
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55
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56 if coding_seq:
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57 if line.endswith(']'):
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58 coding_seq += line[:-1]
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59 co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
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60 coding_seq = ''
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61 else:
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62 coding_seq += line
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63
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64 if args.protein and line.startswith('protein sequence = ['):
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65 if line.endswith(']'):
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66 protein_seq = line[20:-1]
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67 po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
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68 protein_seq = ''
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69 else:
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70 line = line[20:]
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71 protein_seq = line
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72
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73 if args.codingseq and line.startswith('coding sequence = ['):
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74 if line.endswith(']'):
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75 coding_seq = line[19:-1]
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76 co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
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77 coding_seq = ''
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78 else:
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79 line = line[19:]
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80 coding_seq = line
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81
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82 if args.codingseq:
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83 co.close()
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84 if args.protein:
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85 po.close()
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86
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88 if __name__ == '__main__':
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89 parser = argparse.ArgumentParser()
86c89c3bd99d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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90 parser.add_argument('-p', '--protein', help='Path to the protein file.')
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91 parser.add_argument('-c', '--codingseq', help='Path to the coding file.')
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93 args = parser.parse_args()
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94 main( args )