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annotate util/subtools.py @ 0:f493979f1408 draft default tip

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planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author yating-l
date Wed, 21 Dec 2016 12:13:04 -0500
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0
f493979f1408 planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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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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19
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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 stdout = kwargs.get('stdout', subprocess.PIPE)
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32 stderr = kwargs.get('stderr', subprocess.PIPE)
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33 shell = kwargs.get('shell', False)
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34
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35 cmd = array_call[0]
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36
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37 output = None
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38 error = None
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39
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40 # TODO: Check the value of array_call and <=[0]
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41 logging.debug("Calling {0}:".format(cmd))
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42
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43 logging.debug("---------")
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44
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45 # TODO: Use universal_newlines option from Popen?
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46 try:
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47 p = subprocess.Popen(array_call, stdout=stdout, stderr=stderr, shell=shell)
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48
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49 # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
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50
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51 output, error = p.communicate()
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52
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53 if stdout == subprocess.PIPE:
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54 logging.debug("\t{0}".format(output))
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55 else:
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56 logging.debug("\tOutput in file {0}".format(stdout.name))
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57 # If we detect an error from the subprocess, then we raise an exception
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58 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
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59 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
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60 if p.returncode:
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61 if stderr == subprocess.PIPE:
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62 raise PopenError(cmd, error, p.returncode)
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63 else:
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64 # TODO: To Handle properly with a design behind, if we received a option as a file for the error
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65 raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"\
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66 .format(cmd, stderr.name, p.returncode))
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67
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68 except OSError as e:
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69 message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)
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70 if e.filename:
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71 message = '\n'.join((message, ", against this file: {0}".format(e.filename)))
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72 logging.error(message)
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73 sys.exit(-1)
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74 except PopenError as p:
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75 message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)
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76 message = '\n'.join((message, "Its error message is: {0}".format(p.error)))
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77
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78 logging.exception(message)
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80 sys.exit(p.return_code)
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81 except Exception as e:
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82 message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)
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83 logging.exception(message)
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84
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85 sys.exit(-1)
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86 return p
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87
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88 def twoBitInfo(two_bit_file_name, two_bit_info_file):
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89 """
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90 Call twoBitInfo and write the result into twoBit_info_file
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91 :param two_bit_file_name:
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92 :param two_bit_info_file:
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93 :return the subprocess.check_call return object:
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94 """
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95 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
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96 p = _handleExceptionAndCheckCall(array_call)
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97 return p
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98
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99 def faToTwoBit(fasta_file_name, twoBitFile):
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100 """
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101 This function call faToTwoBit UCSC tool, and return the twoBitFile
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102 :param fasta_file_name:
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103 :param mySpecieFolder:
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104 :return:
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105 """
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106
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107 array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
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108 _handleExceptionAndCheckCall(array_call)
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109
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110 return twoBitFile
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111
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112 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):
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113 """
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114 Call gtfToGenePred and write the result into gene_pred_file_name
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115 :param input_gtf_file_name:
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116 :param gene_pred_file_name:
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117 :return:
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118 """
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119 array_call = ['gtfToGenePred', input_gtf_file_name, gene_pred_file_name]
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120 p = _handleExceptionAndCheckCall(array_call)
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121 return p
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122
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123 def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):
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124 """
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125 Call gff3ToGenePred and write the result into gene_pred_file_name
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126 :param input_gff3_file_name:
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127 :param gene_pred_file_name:
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128 :return:
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129 """
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130 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name]
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131 p = _handleExceptionAndCheckCall(array_call)
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132 return p
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133
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134 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
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135 """
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136 Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
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137 :param gene_pred_file_name:
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138 :param unsorted_bigGenePred_file_name:
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139 :return:
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140 """
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141 array_call = ['genePredToBigGenePred',
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142 gene_pred_file_name,
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143 unsorted_bigGenePred_file_name]
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144 p = _handleExceptionAndCheckCall(array_call)
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145 return p
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146
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147 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
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148 """
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149 Call genePredToBed and write the result into unsorted_bed_file_name
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150 :param gene_pred_file_name:
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151 :param unsorted_bed_file_name:
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152 :return:
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153 """
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154 array_call = ['genePredToBed', gene_pred_file_name, unsorted_bed_file_name]
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155 p = _handleExceptionAndCheckCall(array_call)
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156 return p
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157
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158 def sort(unsorted_bed_file_name, sorted_bed_file_name):
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159 """
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160 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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161 :param unsorted_bed_file_name:
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162 :param sorted_bed_file_name:
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163 :return:
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164 """
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165 array_call = ['sort', '-k', '1,1', '-k', '2,2n', unsorted_bed_file_name, '-o', sorted_bed_file_name]
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166 p = _handleExceptionAndCheckCall(array_call)
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167 return p
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168
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169 def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
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170 """
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171 Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
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172 :param two_bit_info_file_name:
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173 :param chrom_sizes_file_name:
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174 :return:
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175 """
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176 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
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177 p = _handleExceptionAndCheckCall(array_call)
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178 return p
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179
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180 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,
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181 typeOption=None, autoSql=None, tab=False):
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182 """
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183 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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184 :param sorted_bed_file_name:
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185 :param chrom_sizes_file_name:
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186 :param big_bed_file_name:
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187 :return:
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188 """
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189
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190 # TODO: Move this into the _handleExceptionAndCheckCall function
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191 # Parse the array
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192 logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))
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193 logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))
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194 logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))
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195 logging.debug("typeOption: {0}".format(typeOption))
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196 logging.debug("autoSql: {0}".format(autoSql))
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197 logging.debug("tab option: {0}".format(tab))
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198
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199 array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
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200 if typeOption:
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201 typeOption = ''.join(['-type=', typeOption])
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202 array_call.append(typeOption)
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203 if autoSql:
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204 autoSql = ''.join(['-as=', autoSql])
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205 array_call.append(autoSql)
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206 if tab:
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207 array_call.append('-tab')
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208
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209 p = _handleExceptionAndCheckCall(array_call)
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210 return p
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211
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212 def sortBam(input_bam_file_name, output_sorted_bam_name):
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213 """
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214 Call samtools on input_bam_file_name and output the result in output_sorted_bam_name
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215 :param input_bam_file_name:
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216 :param output_sorted_bam_name:
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217 :return:
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218 """
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219 array_call = ['samtools', 'sort', input_bam_file_name, '-o', output_sorted_bam_name]
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220 p = _handleExceptionAndCheckCall(array_call)
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221 return p
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222
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223 def createBamIndex(input_sorted_bam_file_name, output_name_index_name):
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224 """
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225 Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name
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226 :param input_sorted_bam_file_name:
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227 :param output_name_index_name:
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228 :return:
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229 """
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230 array_call = ['samtools', 'index', input_sorted_bam_file_name, output_name_index_name]
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231 p = _handleExceptionAndCheckCall(array_call)
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232 return p
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233
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234 def pslToBigPsl(input_psl_file_name, output_bed12_file_name):
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235 """
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236 Call `pslToBigPsl` on input_psl_file_name and output the result in output_bed12_file_name
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237 :param input_psl_file_name: Name of the psl input file
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238 :param output_bed12_file_name: Name of the output file where to store the result of the cmd
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239 :return:
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240 """
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241 # The command to send
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242 array_call = ['pslToBigPsl', input_psl_file_name, output_bed12_file_name]
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243
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244 p = _handleExceptionAndCheckCall(array_call)
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245 return p