Mercurial > repos > yating-l > jbrowsearchivecreator

annotate bedToGff3.py @ 19:df2a55f071fc draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 594c5fa1e3cdb378ecf6b5490ec2cbac5fa8a61e-dirty
author yating-l
date Fri, 07 Jul 2017 15:43:14 -0400
parents 466d52f83079
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2
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3 '''
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4 Convert BED format to gff3
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5 reference for gff3: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
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6 '''
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7 import os
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8 from collections import OrderedDict
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9 import utils
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10
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11 class bedToGff3():
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12 def __init__(self, inputBedFile, chrom_sizes, bed_type, output):
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13 self.input = inputBedFile
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14 #file_dir = os.path.basename(inputBedFile)
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15 #print file_dir + "\n\n"
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16 self.output = output
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17 self.chrom_sizes = chrom_sizes
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18 self.type = bed_type
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19 if self.type == "trfbig":
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20 self.trfbig_to_gff3()
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21 if self.type == "regtools":
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22 self.splicejunctions_to_gff3()
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23 if self.type == "blat":
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24 self.bigpsl_to_gff3()
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25
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26 def trfbig_to_gff3(self):
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27 gff3 = open(self.output, 'w')
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28 gff3.write("##gff-version 3\n")
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29 sizes_dict = utils.sequence_region(self.chrom_sizes)
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30 seq_regions = dict()
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31 with open(self.input, 'r') as bed:
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32 for line in bed:
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33 field = OrderedDict()
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34 attribute = OrderedDict()
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35 li = line.rstrip().split("\t")
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36 field['seqid'] = li[0]
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37 if field['seqid'] not in seq_regions:
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38 end_region = sizes_dict[field['seqid']]
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39 gff3.write("##sequence-region " + field['seqid'] + ' 1 ' + str(end_region) + '\n')
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40 seq_regions[field['seqid']] = end_region
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41 field['source'] = li[3]
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42 field['type'] = 'tandem_repeat'
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43 # The first base in a chromosome is numbered 0 in BED format
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44 field['start'] = str(int(li[1]) + 1)
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45 field['end'] = li[2]
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46 field['score'] = li[9]
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47 field['strand'] = '+'
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48 field['phase'] = '.'
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49 attribute['length of repeat unit'] = li[4]
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50 attribute['mean number of copies of repeat'] = li[5]
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51 attribute['length of consensus sequence'] = li[6]
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52 attribute['percentage match'] = li[7]
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53 attribute['percentage indel'] = li[8]
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54 attribute['percent of a\'s in repeat unit'] = li[10]
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55 attribute['percent of c\'s in repeat unit'] = li[11]
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56 attribute['percent of g\'s in repeat unit'] = li[12]
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57 attribute['percent of t\'s in repeat unit'] = li[13]
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58 attribute['entropy'] = li[14]
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59 attribute['sequence of repeat unit element'] = li[15]
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60 utils.write_features(field, attribute, gff3)
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61 gff3.close()
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62
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63
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64 def splicejunctions_to_gff3(self):
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65 gff3 = open(self.output, 'w')
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66 gff3.write("##gff-version 3\n")
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67 sizes_dict = utils.sequence_region(self.chrom_sizes)
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68 seq_regions = dict()
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69 with open(self.input, 'r') as bed:
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70 for line in bed:
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71 field = OrderedDict()
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72 attribute = OrderedDict()
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73 li = line.rstrip().split("\t")
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74 field['seqid'] = li[0]
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75 if field['seqid'] not in seq_regions:
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76 end_region = sizes_dict[field['seqid']]
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77 gff3.write("##sequence-region " + field['seqid'] + ' 1 ' + str(end_region) + '\n')
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78 seq_regions[field['seqid']] = end_region
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79 field['source'] = li[3]
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80 field['type'] = 'junction'
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81 # The first base in a chromosome is numbered 0 in BED format
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82 field['start'] = int(li[1]) + 1
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83 field['end'] = li[2]
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84 field['score'] = li[12]
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85 field['strand'] = li[5]
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86 field['phase'] = '.'
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87 attribute['ID'] = li[0] + '_' + li[3]
0
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88 attribute['Name'] = li[3]
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89 attribute['blockcount'] = li[9]
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90 attribute['blocksizes'] = li[10]
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91 attribute['chromstarts'] = li[11]
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92 utils.write_features(field, attribute, gff3)
15
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93 utils.child_blocks(field, attribute, gff3, 'exon_junction')
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94 gff3.close()
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95
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96 def bigpsl_to_gff3(self):
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97 gff3 = open(self.output, 'w')
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98 gff3.write("##gff-version 3\n")
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99 sizes_dict = utils.sequence_region(self.chrom_sizes)
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100 seq_regions = dict()
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101 with open(self.input, 'r') as bed:
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102 for line in bed:
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103 field = OrderedDict()
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104 attribute = OrderedDict()
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105 li = line.rstrip().split("\t")
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106 field['seqid'] = li[0]
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107 if field['seqid'] not in seq_regions:
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108 end_region = sizes_dict[field['seqid']]
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109 gff3.write("##sequence-region " + field['seqid'] + ' 1 ' + str(end_region) + '\n')
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110 seq_regions[field['seqid']] = end_region
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111 field['source'] = 'UCSC BLAT alignment tool'
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112 field['type'] = 'match'
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113 # The first base in a chromosome is numbered 0 in BED format
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114 field['start'] = str(int(li[1]) + 1)
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115 field['end'] = li[2]
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116 field['score'] = li[4]
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117 field['strand'] = li[5]
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118 field['phase'] = '.'
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119 attribute['ID'] = li[0] + '_' + li[3]
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120 attribute['Name'] = li[3]
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121 attribute['blockcount'] = li[9]
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122 attribute['blocksizes'] = li[10]
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123 attribute['chromstarts'] = li[11]
18
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124 attribute['ochrom_start'] = li[12]
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125 attribute['ochrom_end'] = li[13]
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126 attribute['ochrom_strand'] = li[14]
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127 attribute['ochrom_size'] = li[15]
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128 attribute['ochrom_starts'] = li[16]
15
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129 attribute['sequence on other chromosome'] = li[17]
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130 attribute['cds in ncbi format'] = li[18]
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131 attribute['size of target chromosome'] = li[19]
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132 attribute['number of bases matched'] = li[20]
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133 attribute['number of bases that don\'t match'] = li[21]
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134 attribute['number of bases that match but are part of repeats'] = li[22]
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135 attribute['number of \'N\' bases'] = li[23]
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136 utils.write_features(field, attribute, gff3)
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137 utils.child_blocks(field, attribute, gff3, 'match_part')
0
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138 gff3.close()
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139