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annotate util/subtools.py @ 28:6aa28a85cc38 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060
author yating-l
date Mon, 10 Jul 2017 17:08:38 -0400
parents df42241d3731
children 7e8a8b732db3
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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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4 """
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rmarenco
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5 This class handles the subprocess calls of the different tools used
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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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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
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yating-l
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14 import tempfile
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16 class PopenError(Exception):
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17 def __init__(self, cmd, error, return_code):
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18 self.cmd = cmd
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19 self.error = error
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20 self.return_code = return_code
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22 def __str__(self):
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23 message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)
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24 message = ','.join((message, "Its error message is: {0}".format(self.error)))
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25 return repr(message)
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27 def _handleExceptionAndCheckCall(array_call, **kwargs):
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28 """
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rmarenco
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29 This class handle exceptions and call the tool.
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30 It maps the signature of subprocess.check_call:
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31 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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32 """
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33 stdout = kwargs.get('stdout', subprocess.PIPE)
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34 stderr = kwargs.get('stderr', subprocess.PIPE)
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35 shell = kwargs.get('shell', False)
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37 cmd = array_call[0]
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38
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39 output = None
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40 error = None
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42 # TODO: Check the value of array_call and <=[0]
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43 logging.debug("Calling {0}:".format(cmd))
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44
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45 logging.debug("---------")
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47 # TODO: Use universal_newlines option from Popen?
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48 try:
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49 p = subprocess.Popen(array_call, stdout=stdout, stderr=stderr, shell=shell)
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51 # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate
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52
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53 output, error = p.communicate()
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54
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55 if stdout == subprocess.PIPE:
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56 logging.debug("\t{0}".format(output))
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57 else:
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58 logging.debug("\tOutput in file {0}".format(stdout.name))
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59 # If we detect an error from the subprocess, then we raise an exception
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60 # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
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61 # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
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62 if p.returncode:
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63 if stderr == subprocess.PIPE:
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64 raise PopenError(cmd, error, p.returncode)
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65 else:
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66 # TODO: To Handle properly with a design behind, if we received a option as a file for the error
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67 raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"\
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68 .format(cmd, stderr.name, p.returncode))
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69
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70 except OSError as e:
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71 message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)
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72 if e.filename:
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73 message = '\n'.join((message, ", against this file: {0}".format(e.filename)))
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74 logging.error(message)
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75 sys.exit(-1)
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76 except PopenError as p:
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77 message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)
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78 message = '\n'.join((message, "Its error message is: {0}".format(p.error)))
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79
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80 logging.exception(message)
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82 sys.exit(p.return_code)
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83 except Exception as e:
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84 message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)
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85 logging.exception(message)
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86
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87 sys.exit(-1)
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88 return p
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89
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90 def twoBitInfo(two_bit_file_name, two_bit_info_file):
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91 """
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92 Call twoBitInfo and write the result into twoBit_info_file
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93 :param two_bit_file_name:
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94 :param two_bit_info_file:
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95 :return the subprocess.check_call return object:
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96 """
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97 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
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98 p = _handleExceptionAndCheckCall(array_call)
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99 return p
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100
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101 def faToTwoBit(fasta_file_name, twoBitFile):
1
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102 """
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103 This function call faToTwoBit UCSC tool, and return the twoBitFile
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104 :param fasta_file_name:
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105 :param mySpecieFolder:
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106 :return:
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107 """
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108
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109 array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
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110 _handleExceptionAndCheckCall(array_call)
1
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111
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112 return twoBitFile
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113
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114 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):
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115 """
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116 Call gtfToGenePred and write the result into gene_pred_file_name
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117 :param input_gtf_file_name:
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118 :param gene_pred_file_name:
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119 :return:
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120 """
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121 array_call = ['gtfToGenePred', input_gtf_file_name, gene_pred_file_name]
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122 p = _handleExceptionAndCheckCall(array_call)
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123 return p
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124
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125 def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):
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126 """
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127 Call gff3ToGenePred and write the result into gene_pred_file_name
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128 :param input_gff3_file_name:
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129 :param gene_pred_file_name:
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130 :return:
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131 """
25
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132 valid_gff3_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gff3")
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133 validateGff(input_gff3_file_name, valid_gff3_file.name)
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134 array_call = ['gff3ToGenePred', valid_gff3_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
13
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138 def genePredToBigGenePred(gene_pred_file_name, unsorted_bigGenePred_file_name):
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139 """
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140 Call genePredToBigGenePred and write the result into unsorted_bigGenePred_file_name
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141 :param gene_pred_file_name:
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142 :param unsorted_bigGenePred_file_name:
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143 :return:
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144 """
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145 array_call = ['genePredToBigGenePred',
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146 gene_pred_file_name,
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147 unsorted_bigGenePred_file_name]
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148 p = _handleExceptionAndCheckCall(array_call)
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149 return p
1
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150
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151 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
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152 """
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153 Call genePredToBed and write the result into unsorted_bed_file_name
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154 :param gene_pred_file_name:
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155 :param unsorted_bed_file_name:
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156 :return:
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157 """
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158 array_call = ['genePredToBed', gene_pred_file_name, unsorted_bed_file_name]
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159 p = _handleExceptionAndCheckCall(array_call)
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160 return p
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161
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162 def sort(unsorted_bed_file_name, sorted_bed_file_name):
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163 """
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164 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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165 :param unsorted_bed_file_name:
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166 :param sorted_bed_file_name:
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167 :return:
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168 """
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169 array_call = ['sort', '-k', '1,1', '-k', '2,2n', unsorted_bed_file_name, '-o', sorted_bed_file_name]
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170 p = _handleExceptionAndCheckCall(array_call)
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171 return p
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172
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173 def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
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174 """
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175 Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
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176 :param two_bit_info_file_name:
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177 :param chrom_sizes_file_name:
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178 :return:
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179 """
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180 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
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181 p = _handleExceptionAndCheckCall(array_call)
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182 return p
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183
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184 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,
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185 typeOption=None, autoSql=None, tab=False, extraIndex=None):
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186 """
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187 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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188 :param sorted_bed_file_name:
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189 :param chrom_sizes_file_name:
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190 :param big_bed_file_name:
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191 :return:
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192 """
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193
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194 # TODO: Move this into the _handleExceptionAndCheckCall function
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195 # Parse the array
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196 logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))
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197 logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))
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198 logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))
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199 logging.debug("typeOption: {0}".format(typeOption))
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200 logging.debug("autoSql: {0}".format(autoSql))
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201 logging.debug("tab option: {0}".format(tab))
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202
1
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203 array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
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204 if typeOption:
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205 typeOption = ''.join(['-type=', typeOption])
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206 array_call.append(typeOption)
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207 if autoSql:
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208 autoSql = ''.join(['-as=', autoSql])
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209 array_call.append(autoSql)
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210 if tab:
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211 array_call.append('-tab')
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212 if extraIndex:
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213 index = ''.join(['-extraIndex=', extraIndex])
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214 array_call.append(index)
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215
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216 p = _handleExceptionAndCheckCall(array_call)
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217 return p
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218
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219 def sortBam(input_bam_file_name, output_sorted_bam_name):
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220 """
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221 Call samtools on input_bam_file_name and output the result in output_sorted_bam_name
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222 :param input_bam_file_name:
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223 :param output_sorted_bam_name:
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224 :return:
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225 """
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226 array_call = ['samtools', 'sort', input_bam_file_name, '-o', output_sorted_bam_name]
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227 p = _handleExceptionAndCheckCall(array_call)
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228 return p
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229
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230 def createBamIndex(input_sorted_bam_file_name, output_name_index_name):
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231 """
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232 Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name
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233 :param input_sorted_bam_file_name:
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234 :param output_name_index_name:
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235 :return:
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236 """
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237 array_call = ['samtools', 'index', input_sorted_bam_file_name, output_name_index_name]
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238 p = _handleExceptionAndCheckCall(array_call)
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239 return p
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240
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241 def pslToBigPsl(input_psl_file_name, output_bed12_file_name):
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242 """
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243 Call `pslToBigPsl` on input_psl_file_name and output the result in output_bed12_file_name
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244 :param input_psl_file_name: Name of the psl input file
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245 :param output_bed12_file_name: Name of the output file where to store the result of the cmd
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246 :return:
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247 """
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248 # The command to send
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249 array_call = ['pslToBigPsl', input_psl_file_name, output_bed12_file_name]
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250
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251 p = _handleExceptionAndCheckCall(array_call)
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252 return p
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253
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254 #santitize trackName. Because track name must begin with a letter and
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255 # contain only the following chars: [a-zA-Z0-9_].
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256 # See the "track" Common settings at:
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257 #https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
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258 def fixName(filename):
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259 if filename == 'cytoBandIdeo':
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260 return filename
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261 valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
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262 sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
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263 sanitize_name = "gonramp_" + sanitize_name
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264 return sanitize_name
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265
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266 def validateGff(orig_gff3, valid_gff3):
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267 """
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268 Remove extra meta line: ##gff-version 3
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269 """
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270 valid = open(valid_gff3, 'w')
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271 num = 0
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272 with open(orig_gff3, 'r') as f:
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273 for line in f:
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274 if '##gff-version 3' in line:
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275 if num == 0:
99dad5f9444c planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 24
diff changeset
276 num += 1
99dad5f9444c planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 24
diff changeset
277 else:
99dad5f9444c planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 24
diff changeset
278 continue
99dad5f9444c planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 24
diff changeset
279 valid.write(line)
99dad5f9444c planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents: 24
diff changeset
280