Mercurial > repos > bgruening > trna_prediction

annotate aragorn_out_to_gff3.py @ 2:358f58401cd6 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
author bgruening
date Wed, 26 Jul 2017 10:14:05 -0400
parents d788d1abe238
children
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1 #!/usr/bin/env python
2
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2 import sys
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3
2
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4 full_gene_model = False
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5 if '--full' in sys.argv:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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6 full_gene_model = True
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7
2
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8 genome_id = None
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9 stdin_data = []
2
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10 KEY_ORDER = ('parent', 'source', 'type', 'start', 'end', 'score', 'strand',
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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11 '8', 'quals')
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12
2
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13 # Table of amino acids
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14 aa_table = {
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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15 'Ala' : 'A',
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16 'Arg' : 'R',
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17 'Asn' : 'N',
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18 'Asp' : 'D',
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19 'Cys' : 'C',
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20 'Gln' : 'Q',
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21 'Glu' : 'E',
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22 'Gly' : 'G',
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23 'His' : 'H',
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24 'Ile' : 'I',
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25 'Leu' : 'L',
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26 'Lys' : 'K',
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27 'Met' : 'M',
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28 'Phe' : 'F',
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29 'Pro' : 'P',
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30 'Ser' : 'S',
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31 'Thr' : 'T',
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32 'Trp' : 'W',
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33 'Tyr' : 'Y',
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34 'Val' : 'V',
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35 'Pyl' : 'O',
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36 'seC' : 'U',
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37 '???' : 'X' }
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38
2
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39 def output_line(gff3):
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40 print '\t'.join(str(gff3[x]) for x in KEY_ORDER)
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41
2
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42 print '##gff-version 3'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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43 for line in sys.stdin:
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44 if line.startswith('>'):
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45 genome_id = line[1:].strip()
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46 if ' ' in genome_id:
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47 genome_id = genome_id[0:genome_id.index(' ')]
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48 else:
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49 data = line.split()
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50 if len(data) == 5:
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51 # Parse data
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52 strand = '-' if data[2].startswith('c') else '+'
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53 start, end = data[2][data[2].index('[') + 1:-1].split(',')
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54
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55 gff3 = {
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56 'parent': genome_id,
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57 'source': 'aragorn',
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58 'start': int(start),
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59 'end': int(end),
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60 'strand': strand,
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61 'score': '.',
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62 '8': '.',
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63 }
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64
2
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65 aa_long = data[1][5:]
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66 aa_short = aa_table[aa_long]
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67 anticodon = data[4][1:data[4].index(")")].upper().replace("T", "U")
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68 name = 'trn{}-{}'.format(aa_short, anticodon)
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69
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70 if not full_gene_model:
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71 gff3.update({
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72 'type': 'tRNA',
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73 'quals': 'ID=tRNA{0}.{1};Name={name};product={2}'.format(genome_id, *data, name = name),
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74 })
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75 output_line(gff3)
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76 else:
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77 gff3.update({
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78 'type': 'gene',
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79 'quals': 'ID=gene{0}.{1};Name={name};product={2}'.format(genome_id, *data, name = name),
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80 })
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81 output_line(gff3)
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82 gff3.update({
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83 'type': 'tRNA',
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84 'quals': 'ID=tRNA{0}.{1};Parent=gene{0}.{1};Name={name};product={2}'.format(genome_id, *data, name = name),
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85 })
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86 output_line(gff3)
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87
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88 # If no introns
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89 if ')i(' not in data[4]:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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90 gff3['type'] = 'exon'
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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91 gff3['quals'] = 'Parent=tRNA{0}.{1}'.format(genome_id, *data)
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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92 output_line(gff3)
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93 else:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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94 intron_location = data[4][data[4].rindex('(') + 1:-1].split(',')
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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95 intron_start, intron_length = map(int, intron_location)
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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96 if strand == '+':
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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97 original_end = gff3['end']
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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98 else:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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99 original_end = gff3['start']
1
d788d1abe238 Uploaded
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100
2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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101 # EXON
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102 gff3.update({
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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103 'type': 'exon',
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104 'quals': 'Parent=tRNA{0}.{1}'.format(genome_id, *data),
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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105 })
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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106 if strand == '+':
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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107 gff3['end'] = gff3['start'] + intron_start - 2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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108 else:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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109 gff3['start'] = gff3['end'] - intron_start + 2
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110
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111 output_line(gff3)
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112
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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113 # INTRON
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114 gff3.update({
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115 'type': 'intron',
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116 'quals': 'Parent=tRNA{0}.{1}'.format(genome_id, *data),
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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117 })
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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118 if strand == '+':
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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119 gff3['start'] = gff3['end'] + 1
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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120 gff3['end'] = gff3['start'] + intron_length + 2
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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121 else:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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122 gff3['end'] = gff3['start'] - 1
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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123 gff3['start'] = gff3['end'] - intron_length + 1
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124
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125 output_line(gff3)
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126
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127 # EXON
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128 gff3.update({
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129 'type': 'exon',
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130 'quals': 'Parent=tRNA{0}.{1}'.format(genome_id, *data),
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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131 })
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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132 if strand == '+':
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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133 gff3['start'] = gff3['end'] + 1
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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134 gff3['end'] = original_end
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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135 else:
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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136 gff3['end'] = gff3['start'] - 1
358f58401cd6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
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137 gff3['start'] = original_end
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138
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139 output_line(gff3)