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annotate util/subtools.py @ 85:a65e52152476 draft default tip

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Mon, 06 Nov 2017 13:13:01 -0500
parents 4ca7cbf2d9b8
children
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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 import string
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14 import tempfile
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15
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17 class PopenError(Exception):
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18 def __init__(self, cmd, error, return_code):
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19 self.cmd = cmd
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20 self.error = error
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21 self.return_code = return_code
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23 def __str__(self):
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24 message = "The subprocess {0} has returned the error: {1}.".format(
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25 self.cmd, self.return_code)
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26 message = ','.join(
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27 (message, "Its error message is: {0}".format(self.error)))
0
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28 return repr(message)
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31 def _handleExceptionAndCheckCall(array_call, **kwargs):
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32 """
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33 This class handle exceptions and call the tool.
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34 It maps the signature of subprocess.check_call:
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35 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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36 """
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37 stdout = kwargs.get('stdout', subprocess.PIPE)
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38 stderr = kwargs.get('stderr', subprocess.PIPE)
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39 shell = kwargs.get('shell', False)
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41 cmd = array_call[0]
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42
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43 output = None
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44 error = None
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46 # TODO: Check the value of array_call and <=[0]
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47 logging.debug("Calling {0}:".format(cmd))
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48 logging.debug("%s", array_call)
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49 logging.debug("---------")
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50
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51 # TODO: Use universal_newlines option from Popen?
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52 try:
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53 p = subprocess.Popen(array_call, stdout=stdout,
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54 stderr=stderr, shell=shell)
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56 # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
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57
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58 output, error = p.communicate()
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59
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60 if stdout == subprocess.PIPE:
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61 logging.debug("\t{0}".format(output))
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62 else:
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63 logging.debug("\tOutput in file {0}".format(stdout.name))
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64 # If we detect an error from the subprocess, then we raise an exception
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65 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
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66 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
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67 if p.returncode:
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68 if stderr == subprocess.PIPE:
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69 raise PopenError(cmd, error, p.returncode)
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70 else:
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71 # TODO: To Handle properly with a design behind, if we received a option as a file for the error
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72 raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"
0
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73 .format(cmd, stderr.name, p.returncode))
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74
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75 except OSError as e:
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76 message = "The subprocess {0} has encountered an OSError: {1}".format(
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77 cmd, e.strerror)
0
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78 if e.filename:
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79 message = '\n'.join(
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80 (message, ", against this file: {0}".format(e.filename)))
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81 logging.error(message)
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82 sys.exit(-1)
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83 except PopenError as p:
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84 message = "The subprocess {0} has returned the error: {1}.".format(
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85 p.cmd, p.return_code)
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86 message = '\n'.join(
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87 (message, "Its error message is: {0}".format(p.error)))
0
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88
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89 logging.exception(message)
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90
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91 sys.exit(p.return_code)
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92 except Exception as e:
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93 message = "The subprocess {0} has encountered an unknown error: {1}".format(
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94 cmd, e)
0
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95 logging.exception(message)
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96
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97 sys.exit(-1)
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98 return p
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99
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100
0
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101 def twoBitInfo(two_bit_file_name, two_bit_info_file):
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102 """
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103 Call twoBitInfo and write the result into twoBit_info_file
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104 :param two_bit_file_name:
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105 :param two_bit_info_file:
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106 :return the subprocess.check_call return object:
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107 """
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108 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
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109 p = _handleExceptionAndCheckCall(array_call)
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110 return p
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111
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112
0
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113 def faToTwoBit(fasta_file_name, twoBitFile):
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114 """
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115 This function call faToTwoBit UCSC tool, and return the twoBitFile
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116 :param fasta_file_name:
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117 :param mySpecieFolder:
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118 :return:
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119 """
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120
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121 array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
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122 _handleExceptionAndCheckCall(array_call)
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123
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124 return twoBitFile
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125
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126
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127 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):
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128 """
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129 Call gtfToGenePred and write the result into gene_pred_file_name
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130 :param input_gtf_file_name:
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131 :param gene_pred_file_name:
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132 :return:
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133 """
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134 array_call = ['gtfToGenePred', input_gtf_file_name, gene_pred_file_name]
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135 p = _handleExceptionAndCheckCall(array_call)
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136 return p
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137
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138
0
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139 def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):
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140 """
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141 Call gff3ToGenePred and write the result into gene_pred_file_name
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142 :param input_gff3_file_name:
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143 :param gene_pred_file_name:
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144 :return:
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145 """
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146 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name]
0
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147 p = _handleExceptionAndCheckCall(array_call)
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148 return p
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149
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150
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151 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
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152 """
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153 Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
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154 :param gene_pred_file_name:
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155 :param unsorted_bigGenePred_file_name:
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156 :return:
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157 """
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158 array_call = ['genePredToBigGenePred',
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159 gene_pred_file_name,
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160 unsorted_bigGenePred_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 genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
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166 """
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167 Call genePredToBed and write the result into unsorted_bed_file_name
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168 :param gene_pred_file_name:
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169 :param unsorted_bed_file_name:
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170 :return:
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171 """
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172 array_call = ['genePredToBed', gene_pred_file_name, unsorted_bed_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
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177 def sort(unsorted_bed_file_name, sorted_bed_file_name):
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178 """
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179 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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180 :param unsorted_bed_file_name:
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181 :param sorted_bed_file_name:
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182 :return:
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183 """
66
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184 array_call = ['sort', '-k', '1,1', '-k', '2,2n',
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185 unsorted_bed_file_name, '-o', sorted_bed_file_name]
0
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186 p = _handleExceptionAndCheckCall(array_call)
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187 return p
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188
66
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189
0
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190 def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
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191 """
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192 Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
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193 :param two_bit_info_file_name:
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194 :param chrom_sizes_file_name:
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195 :return:
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196 """
66
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197 array_call = ['sort', '-k2rn', two_bit_info_file_name,
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198 '-o', chrom_sizes_file_name]
0
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199 p = _handleExceptionAndCheckCall(array_call)
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200 return p
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201
66
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202
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203 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name, options=None):
0
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204 """
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205 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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206 :param sorted_bed_file_name:
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207 :param chrom_sizes_file_name:
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208 :param big_bed_file_name:
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209 :return:
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210 """
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211
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212 array_call = ['bedToBigBed', sorted_bed_file_name,
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213 chrom_sizes_file_name, big_bed_file_name]
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214 if options:
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215 typeOption = options.get("typeOption")
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216 autoSql = options.get("autoSql")
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217 tab = options.get("tab")
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218 extraIndex = options.get("extraIndex")
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219 if typeOption:
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220 typeOption = ''.join(['-type=', typeOption])
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221 array_call.append(typeOption)
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222 if autoSql:
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223 autoSql = ''.join(['-as=', autoSql])
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224 array_call.append(autoSql)
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225 if tab:
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226 array_call.append('-tab')
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227 if extraIndex:
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228 index = ''.join(['-extraIndex=', extraIndex])
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229 array_call.append(index)
0
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230 p = _handleExceptionAndCheckCall(array_call)
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231 return p
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232
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233 def sortBam(input_bam_file_name, output_sorted_bam_name):
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234 """
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235 Call samtools on input_bam_file_name and output the result in output_sorted_bam_name
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236 :param input_bam_file_name:
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237 :param output_sorted_bam_name:
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238 :return:
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239 """
66
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240 array_call = ['samtools', 'sort',
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241 input_bam_file_name, '-o', output_sorted_bam_name]
0
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242 p = _handleExceptionAndCheckCall(array_call)
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243 return p
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244
66
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245
0
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246 def createBamIndex(input_sorted_bam_file_name, output_name_index_name):
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247 """
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248 Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name
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249 :param input_sorted_bam_file_name:
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250 :param output_name_index_name:
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251 :return:
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252 """
66
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253 array_call = ['samtools', 'index',
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254 input_sorted_bam_file_name, output_name_index_name]
0
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255 p = _handleExceptionAndCheckCall(array_call)
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256 return p
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257
66
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258
0
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259 def pslToBigPsl(input_psl_file_name, output_bed12_file_name):
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260 """
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261 Call `pslToBigPsl` on input_psl_file_name and output the result in output_bed12_file_name
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262 :param input_psl_file_name: Name of the psl input file
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263 :param output_bed12_file_name: Name of the output file where to store the result of the cmd
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264 :return:
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265 """
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266 # The command to send
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267 array_call = ['pslToBigPsl', input_psl_file_name, output_bed12_file_name]
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268
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269 p = _handleExceptionAndCheckCall(array_call)
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270 return p
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271
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272 # santitize trackName. Because track name must begin with a letter and
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273 # contain only the following chars: [a-zA-Z0-9_].
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274 # See the "track" Common settings at:
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275 # https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
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276
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277 def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):
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278 """
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279 Call validateFiles on input_file, using chrom_sizes_file_name and file_type
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280 :param input_file:
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281 :param chrom_sizes_file_name:
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282 :param file_type:
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283 :return:
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284 """
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285
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286 array_call = ['validateFiles', '-chromInfo=' + chrom_sizes_file_name, '-type='+ file_type, input_file]
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287 if options:
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288 tab = options.get("tab")
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289 autoSql = options.get("autoSql")
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290 logging.debug("tab: {0}".format(tab))
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291 logging.debug("autoSql: {0}".format(autoSql))
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292 if autoSql:
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293 autoSql = ''.join(['-as=', autoSql])
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294 array_call.append(autoSql)
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295 if tab:
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296 array_call.append('-tab')
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297 p = _handleExceptionAndCheckCall(array_call)
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298 return p
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299
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300 def pslCheck(input_file, options=None):
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301 """
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302 Call pslCheck on input_file
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303 :param input_file:
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304 :return:
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305 """
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306
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307 array_call = ['pslCheck', input_file]
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308 p = _handleExceptionAndCheckCall(array_call)
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309 return p
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310
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312