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annotate util/subtools.py @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents acc233161f50
children 3233451a3bd6
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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4 """
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5 This class handles the subprocess calls of the different tools used
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6 in HubArchiveCreator
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7 """
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8
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9 import logging
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10 import os
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11 import subprocess
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12 import sys
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13
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14 class PopenError(Exception):
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15 def __init__(self, cmd, error, return_code):
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16 self.cmd = cmd
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17 self.error = error
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18 self.return_code = return_code
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20 def __str__(self):
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21 message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)
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22 message = ','.join((message, "Its error message is: {0}".format(self.error)))
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23 return repr(message)
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25 def _handleExceptionAndCheckCall(array_call, **kwargs):
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26 """
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27 This class handle exceptions and call the tool.
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28 It maps the signature of subprocess.check_call:
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29 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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30 """
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31 stdin = kwargs.get('stdin')
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32 stdout = kwargs.get('stdout')
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33 stderr = kwargs.get('stderr')
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34 shell = kwargs.get('shell')
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36 cmd = array_call[0]
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38 output = None
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39 error = None
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41 # TODO: Check the value of array_call and <=[0]
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42 logging.debug("Calling {0}:".format(cmd))
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44 logging.debug("---------")
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46 # TODO: Use universal_newlines option from Popen?
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47 try:
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48 p = subprocess.Popen(array_call, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=shell)
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49 output, error = p.communicate()
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51 logging.debug("\t{0}".format(output))
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52 # If we detect an error from the subprocess, then we raise an exception
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53 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
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54 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
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55 if p.returncode:
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56 raise PopenError(cmd, error, p.returncode)
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57
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58 except OSError as e:
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59 message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)
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60 if e.filename:
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61 message = '\n'.join((message, ", against this file: {0}".format(e.filename)))
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62 logging.error(message)
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63 sys.exit(-1)
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64 except PopenError as p:
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65 message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)
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66 message = '\n'.join((message, "Its error message is: {0}".format(p.error)))
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68 logging.exception(message)
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70 sys.exit(p.return_code)
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71 except Exception as e:
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72 message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)
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73 logging.exception(message)
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75 sys.exit(-1)
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76 return p
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79 def twoBitInfo(two_bit_file_name, two_bit_info_file):
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80 """
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81 Call twoBitInfo and write the result into twoBit_info_file
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82 :param two_bit_file_name:
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83 :param two_bit_info_file:
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84 :return the subprocess.check_call return object:
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85 """
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86 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
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87 p = _handleExceptionAndCheckCall(array_call)
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88 return p
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90
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91 def faToTwoBit(fasta_file_name, twoBitFile):
1
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92 """
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93 This function call faToTwoBit UCSC tool, and return the twoBitFile
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94 :param fasta_file_name:
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95 :param mySpecieFolder:
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96 :return:
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97 """
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98
10
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99 array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
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100 _handleExceptionAndCheckCall(array_call)
1
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101
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102 return twoBitFile
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103
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104
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105 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):
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106 """
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107 Call gtfToGenePred and write the result into gene_pred_file_name
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108 :param input_gtf_file_name:
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109 :param gene_pred_file_name:
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110 :return:
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111 """
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112 array_call = ['gtfToGenePred', input_gtf_file_name, gene_pred_file_name]
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113 p = _handleExceptionAndCheckCall(array_call)
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114 return p
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115
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116
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117 def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):
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118 """
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119 Call gff3ToGenePred and write the result into gene_pred_file_name
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120 :param input_gff3_file_name:
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121 :param gene_pred_file_name:
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122 :return:
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123 """
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124 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name]
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125 p = _handleExceptionAndCheckCall(array_call)
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126 return p
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127
13
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128 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
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129 """
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130 Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
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131 :param gene_pred_file_name:
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132 :param unsorted_bigGenePred_file_name:
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133 :return:
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134 """
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135 array_call = ['genePredToBigGenePred',
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136 gene_pred_file_name,
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137 unsorted_bigGenePred_file_name]
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138 p = _handleExceptionAndCheckCall(array_call)
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139 return p
1
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140
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141 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
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142 """
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143 Call genePredToBed and write the result into unsorted_bed_file_name
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144 :param gene_pred_file_name:
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145 :param unsorted_bed_file_name:
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146 :return:
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147 """
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148 array_call = ['genePredToBed', gene_pred_file_name, unsorted_bed_file_name]
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149 p = _handleExceptionAndCheckCall(array_call)
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150 return p
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151
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152
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153 def sort(unsorted_bed_file_name, sorted_bed_file_name):
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154 """
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155 Call sort with -k1,1 -k2,2n on unsorted_bed_file_name and write the result into sorted_bed_file_name
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156 :param unsorted_bed_file_name:
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157 :param sorted_bed_file_name:
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158 :return:
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159 """
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160 array_call = ['sort', '-k', '1,1', '-k', '2,2n', unsorted_bed_file_name, '-o', sorted_bed_file_name]
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161 p = _handleExceptionAndCheckCall(array_call)
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162 return p
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163
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164
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165 def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
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166 """
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167 Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
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168 :param two_bit_info_file_name:
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169 :param chrom_sizes_file_name:
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170 :return:
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171 """
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172 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
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173 p = _handleExceptionAndCheckCall(array_call)
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174 return p
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175
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176
13
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177 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,
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178 typeOption=None, autoSql=None, tab=False):
1
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179 """
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180 Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name
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181 :param sorted_bed_file_name:
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182 :param chrom_sizes_file_name:
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183 :param big_bed_file_name:
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184 :return:
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185 """
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186
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187 # TODO: Move this into the _handleExceptionAndCheckCall function
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188 # Parse the array
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189 logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))
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190 logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))
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191 logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))
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192 logging.debug("typeOption: {0}".format(typeOption))
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193 logging.debug("autoSql: {0}".format(autoSql))
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194 logging.debug("tab option: {0}".format(tab))
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195
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196 array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
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197 if typeOption:
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198 typeOption = ''.join(['-type=', typeOption])
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199 array_call.append(typeOption)
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200 if autoSql:
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201 autoSql = ''.join(['-as=', autoSql])
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202 array_call.append(autoSql)
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203 if tab:
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204 array_call.append('-tab')
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205
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206 p = _handleExceptionAndCheckCall(array_call)
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207 return p
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208
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209
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210 def sortBam(input_bam_file_name, output_sorted_bam_name):
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211 """
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212 Call samtools on input_bam_file_name and output the result in output_sorted_bam_name
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213 :param input_bam_file_name:
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214 :param output_sorted_bam_name:
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215 :return:
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216 """
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217 array_call = ['samtools', 'sort', input_bam_file_name, '-o', output_sorted_bam_name]
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218 p = _handleExceptionAndCheckCall(array_call)
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219 return p
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220
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221
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222 def createBamIndex(input_sorted_bam_file_name, output_name_index_name):
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223 """
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224 Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name
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225 :param input_sorted_bam_file_name:
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226 :param output_name_index_name:
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227 :return:
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228 """
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229 array_call = ['samtools', 'index', input_sorted_bam_file_name, output_name_index_name]
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230 p = _handleExceptionAndCheckCall(array_call)
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231 return p