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annotate util/subtools.py @ 24:fcc1021bd496 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
author yating-l
date Wed, 31 May 2017 11:35:16 -0400
parents 884ee2a71680
children 99dad5f9444c
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rmarenco
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1 #!/usr/bin/python
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rmarenco
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2 # -*- coding: utf8 -*-
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rmarenco
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4 """
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rmarenco
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5 This class handles the subprocess calls of the different tools used
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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6 in HubArchiveCreator
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7 """
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8
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rmarenco
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9 import logging
1
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rmarenco
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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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yating-l
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13 import string
1
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14
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15 class PopenError(Exception):
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16 def __init__(self, cmd, error, return_code):
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17 self.cmd = cmd
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18 self.error = error
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19 self.return_code = return_code
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21 def __str__(self):
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22 message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)
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23 message = ','.join((message, "Its error message is: {0}".format(self.error)))
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24 return repr(message)
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26 def _handleExceptionAndCheckCall(array_call, **kwargs):
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27 """
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rmarenco
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28 This class handle exceptions and call the tool.
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29 It maps the signature of subprocess.check_call:
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30 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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31 """
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32 stdout = kwargs.get('stdout', subprocess.PIPE)
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33 stderr = kwargs.get('stderr', subprocess.PIPE)
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34 shell = kwargs.get('shell', False)
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36 cmd = array_call[0]
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37
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38 output = None
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39 error = None
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40
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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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43
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44 logging.debug("---------")
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45
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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=stdout, stderr=stderr, shell=shell)
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49
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50 # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
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51
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52 output, error = p.communicate()
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53
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54 if stdout == subprocess.PIPE:
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55 logging.debug("\t{0}".format(output))
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56 else:
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57 logging.debug("\tOutput in file {0}".format(stdout.name))
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58 # If we detect an error from the subprocess, then we raise an exception
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59 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
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60 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
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61 if p.returncode:
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62 if stderr == subprocess.PIPE:
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63 raise PopenError(cmd, error, p.returncode)
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64 else:
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65 # TODO: To Handle properly with a design behind, if we received a option as a file for the error
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66 raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"\
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67 .format(cmd, stderr.name, p.returncode))
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68
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69 except OSError as e:
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70 message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)
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71 if e.filename:
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72 message = '\n'.join((message, ", against this file: {0}".format(e.filename)))
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73 logging.error(message)
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74 sys.exit(-1)
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75 except PopenError as p:
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76 message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)
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77 message = '\n'.join((message, "Its error message is: {0}".format(p.error)))
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78
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79 logging.exception(message)
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81 sys.exit(p.return_code)
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82 except Exception as e:
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83 message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)
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84 logging.exception(message)
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85
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86 sys.exit(-1)
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87 return p
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88
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89 def twoBitInfo(two_bit_file_name, two_bit_info_file):
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90 """
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91 Call twoBitInfo and write the result into twoBit_info_file
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92 :param two_bit_file_name:
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93 :param two_bit_info_file:
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94 :return the subprocess.check_call return object:
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95 """
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96 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
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97 p = _handleExceptionAndCheckCall(array_call)
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98 return p
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99
10
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100 def faToTwoBit(fasta_file_name, twoBitFile):
1
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101 """
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102 This function call faToTwoBit UCSC tool, and return the twoBitFile
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103 :param fasta_file_name:
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104 :param mySpecieFolder:
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105 :return:
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106 """
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107
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108 array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
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109 _handleExceptionAndCheckCall(array_call)
1
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110
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111 return twoBitFile
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112
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113 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):
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114 """
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115 Call gtfToGenePred and write the result into gene_pred_file_name
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116 :param input_gtf_file_name:
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117 :param gene_pred_file_name:
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118 :return:
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119 """
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120 array_call = ['gtfToGenePred', input_gtf_file_name, gene_pred_file_name]
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121 p = _handleExceptionAndCheckCall(array_call)
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122 return p
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123
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124 def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):
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125 """
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126 Call gff3ToGenePred and write the result into gene_pred_file_name
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127 :param input_gff3_file_name:
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128 :param gene_pred_file_name:
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129 :return:
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130 """
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131 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name]
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132 p = _handleExceptionAndCheckCall(array_call)
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133 return p
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134
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135 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
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136 """
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137 Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
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138 :param gene_pred_file_name:
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139 :param unsorted_bigGenePred_file_name:
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140 :return:
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141 """
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142 array_call = ['genePredToBigGenePred',
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143 gene_pred_file_name,
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144 unsorted_bigGenePred_file_name]
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145 p = _handleExceptionAndCheckCall(array_call)
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146 return p
1
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147
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148 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
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149 """
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150 Call genePredToBed and write the result into unsorted_bed_file_name
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151 :param gene_pred_file_name:
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152 :param unsorted_bed_file_name:
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153 :return:
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154 """
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155 array_call = ['genePredToBed', gene_pred_file_name, unsorted_bed_file_name]
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156 p = _handleExceptionAndCheckCall(array_call)
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157 return p
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158
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159 def sort(unsorted_bed_file_name, sorted_bed_file_name):
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160 """
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161 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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162 :param unsorted_bed_file_name:
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163 :param sorted_bed_file_name:
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164 :return:
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165 """
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166 array_call = ['sort', '-k', '1,1', '-k', '2,2n', unsorted_bed_file_name, '-o', sorted_bed_file_name]
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167 p = _handleExceptionAndCheckCall(array_call)
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168 return p
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169
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170 def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
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171 """
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172 Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
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173 :param two_bit_info_file_name:
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174 :param chrom_sizes_file_name:
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175 :return:
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176 """
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177 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
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178 p = _handleExceptionAndCheckCall(array_call)
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179 return p
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180
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181 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,
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182 typeOption=None, autoSql=None, tab=False):
1
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183 """
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184 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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185 :param sorted_bed_file_name:
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186 :param chrom_sizes_file_name:
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187 :param big_bed_file_name:
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188 :return:
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189 """
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190
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191 # TODO: Move this into the _handleExceptionAndCheckCall function
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192 # Parse the array
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193 logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))
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194 logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))
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195 logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))
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196 logging.debug("typeOption: {0}".format(typeOption))
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197 logging.debug("autoSql: {0}".format(autoSql))
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198 logging.debug("tab option: {0}".format(tab))
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199
1
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200 array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
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201 if typeOption:
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202 typeOption = ''.join(['-type=', typeOption])
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203 array_call.append(typeOption)
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204 if autoSql:
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205 autoSql = ''.join(['-as=', autoSql])
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206 array_call.append(autoSql)
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207 if tab:
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208 array_call.append('-tab')
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209
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210 p = _handleExceptionAndCheckCall(array_call)
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211 return p
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212
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213 def sortBam(input_bam_file_name, output_sorted_bam_name):
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214 """
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215 Call samtools on input_bam_file_name and output the result in output_sorted_bam_name
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216 :param input_bam_file_name:
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217 :param output_sorted_bam_name:
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218 :return:
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219 """
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220 array_call = ['samtools', 'sort', input_bam_file_name, '-o', output_sorted_bam_name]
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221 p = _handleExceptionAndCheckCall(array_call)
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222 return p
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223
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224 def createBamIndex(input_sorted_bam_file_name, output_name_index_name):
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225 """
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226 Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name
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227 :param input_sorted_bam_file_name:
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228 :param output_name_index_name:
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229 :return:
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230 """
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231 array_call = ['samtools', 'index', input_sorted_bam_file_name, output_name_index_name]
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232 p = _handleExceptionAndCheckCall(array_call)
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233 return p
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234
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235 def pslToBigPsl(input_psl_file_name, output_bed12_file_name):
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236 """
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237 Call `pslToBigPsl` on input_psl_file_name and output the result in output_bed12_file_name
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238 :param input_psl_file_name: Name of the psl input file
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239 :param output_bed12_file_name: Name of the output file where to store the result of the cmd
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240 :return:
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241 """
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242 # The command to send
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243 array_call = ['pslToBigPsl', input_psl_file_name, output_bed12_file_name]
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244
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245 p = _handleExceptionAndCheckCall(array_call)
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246 return p
21
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247
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248 #santitize trackName. Because track name must begin with a letter and
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249 # contain only the following chars: [a-zA-Z0-9_].
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250 # See the "track" Common settings at:
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251 #https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
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252 def fixName(filename):
24
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253 if filename == 'cytoBandIdeo':
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254 return filename
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255 valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
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256 sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
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257 sanitize_name = "gonramp_" + sanitize_name
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258 return sanitize_name