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annotate utils.py @ 62:86d6f50870dd draft default tip

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 79699b5964c673b7eb815b4d669ab7f07ea2068a-dirty
author yating-l
date Tue, 11 Apr 2017 16:08:57 -0400
parents 3e5b6f6a9abe
children
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1 #!/usr/bin/env python
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2
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3 """
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4 This file include common used functions for converting file format to gff3
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5 """
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6 from collections import OrderedDict
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7 import json
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8 import subprocess
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9 import os
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10 import tempfile
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11 import string
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13 def write_features(field, attribute, gff3):
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14 """
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15 The function write the features to gff3 format (defined in https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
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16 field, attribute are ordered dictionary
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17 gff3 is the file handler
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18 """
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19 attr = []
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20 for v in field.values():
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21 gff3.write(str(v) + '\t')
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22 for k, v in attribute.items():
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23 s = str(k) + '=' + str(v)
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24 attr.append(s)
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25 gff3.write(';'.join(attr))
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26 gff3.write('\n')
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28 def getChromSizes(reference, tool_dir):
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29 #TODO: find a better way instead of shipping the two exec files with the tool
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30 faToTwoBit = os.path.join(tool_dir, 'faToTwoBit')
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31 twoBitInfo = os.path.join(tool_dir, 'twoBitInfo')
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32 try:
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33 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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34 chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0, suffix='.chrom.sizes', delete=False)
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35 except IOError as err:
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36 print "Cannot create tempfile err({0}): {1}".format(err.errno, err.strerror)
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37 try:
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38 subprocess.call(['faToTwoBit', reference, twoBitFile.name])
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39 except OSError as err:
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40 print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
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41 try:
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42 subprocess.call(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
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43 except OSError as err:
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44 print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
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45 return chrom_sizes
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47 def sequence_region(chrom_sizes):
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48 """
0
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49 This function read from a chromatin size file generated by twoBitInfo and write the information to dict
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50 return a dict
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51 """
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52 f = open(chrom_sizes, 'r')
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53 sizes = f.readlines()
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54 sizes_dict = {}
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55 for line in sizes:
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56 chrom_info = line.rstrip().split('\t')
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57 sizes_dict[chrom_info[0]] = chrom_info[1]
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58 return sizes_dict
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59
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60 def child_blocks(parent_field, parent_attr, gff3):
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61 num = 0
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62 blockcount = int(parent_attr['blockcount'])
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63 chromstart = parent_attr['chromstarts'].split(',')
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64 blocksize = parent_attr['blocksizes'].split(',')
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65 while num < blockcount:
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66 child_attr = OrderedDict()
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67 child_field = parent_field
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68 child_field['type'] = 'exon_junction'
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69 child_field['start'] = int(chromstart[num]) + int(parent_field['start'])
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70 child_field['end'] = int(child_field['start']) + int(blocksize[num]) - 1
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71 child_attr['ID'] = parent_attr['ID'] + '_exon_' + str(num+1)
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72 child_attr['Parent'] = parent_attr['ID']
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73 write_features(child_field, child_attr, gff3)
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74 num = num + 1
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75
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76 def add_tracks_to_json(trackList_json, new_tracks, modify_type):
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77 """
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78 Add to track configuration (trackList.json)
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79 # modify_type = 'add_tracks': add a new track like bam or bigwig, new_track = dict()
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80 # modify_type = 'add_attr': add configuration to the existing track, new_track = dict(track_name: dict())
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81 """
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82 with open(trackList_json, 'r+') as f:
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83 data = json.load(f)
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84 if modify_type == 'add_tracks':
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85 data['tracks'].append(new_tracks)
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86 elif modify_type == 'add_attr':
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87 for k in new_tracks:
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88 for track in data['tracks']:
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89 if k.lower() in track['urlTemplate'].lower():
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90 attr = new_tracks[k]
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91 for k, v in attr.items():
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92 track[k] = v
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93 f.seek(0, 0)
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94 f.write(json.dumps(data, separators=(',' , ':'), indent=4))
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95 f.truncate()
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96 f.close()
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97
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98 def gtfToGff3(gtf_file, gff3_file, chrom_sizes):
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99 """
0
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100 Covert gtf file output from StringTie to gff3 format
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101 """
0
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102 gff3 = open(gff3_file, 'w')
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103 gff3.write("##gff-version 3\n")
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104 sizes_dict = sequence_region(chrom_sizes)
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105 seq_regions = dict()
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106 parents = dict()
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107 with open(gtf_file, 'r') as gtf:
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108 for line in gtf:
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109 if line.startswith('#'):
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110 continue
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111 field = OrderedDict()
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112 attribute = OrderedDict()
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113 li = line.rstrip().split("\t")
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114 #print li
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115 field['seqid'] = li[0]
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116 #print field['seqid']
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117 if field['seqid'] not in seq_regions:
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118 end_region = sizes_dict[field['seqid']]
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119 gff3.write("##sequence-region " + field['seqid'] + ' 1 ' + str(end_region) + '\n')
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120 seq_regions[field['seqid']] = end_region
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121 field['source'] = li[1]
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122 field['type'] = li[2]
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123 # The first base in a chromosome is numbered 0 in BED format
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124 field['start'] = li[3]
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125 field['end'] = li[4]
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126 field['score'] = li[5]
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127 field['strand'] = li[6]
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128 field['phase'] = li[7]
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129 attr_li = li[8].split(';')
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130 gene_id = attr_li[0].split()[1].strip('"')
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131 attribute['ID'] = gene_id + '_' + field['type'] + '_' + str(field['start']) + '_' + str(field['end'])
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132 if field['type'] == 'transcript':
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133 parents[gene_id] = attribute['ID']
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134 attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
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135 attribute['coverage'] = attr_li[2].split()[1].strip('"')
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136 attribute['fpkm'] = attr_li[3].split()[1].strip('"')
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137 attribute['tpm'] = attr_li[4].split()[1].strip('"')
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138 elif field['type'] == 'exon':
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139 attribute['Parent'] = parents[gene_id]
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140 attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
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141 attribute['coverage'] = attr_li[3].split()[1].strip('"')
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142 write_features(field, attribute, gff3)
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143 gff3.close()
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144
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145
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146 def sanitize_name(input_name):
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147 """
5
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148 Galaxy will name all the files and dirs as *.dat,
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149 the function can replace '.' to '_' for the dirs
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150 """
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151 validChars = "_-%s%s" % (string.ascii_letters, string.digits)
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152 sanitized_name = ''.join([c if c in validChars else '_' for c in input_name])
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153 return "gonramp_" + sanitized_name
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154
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155 def createBamIndex(bamfile):
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156 subprocess.call(['samtools', 'index', bamfile])
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157 filename = bamfile + '.bai'
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158 if os.path.exists(filename):
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159 return filename
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160 else:
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161 raise ValueError('Did not find bai file')