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annotate util/subtools.py @ 2:df9e12da0d13 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Thu, 14 Jul 2016 12:49:51 -0400
parents fb5e60d4d18a
children acc233161f50
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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 os
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10 import subprocess
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13 def _handleExceptionAndCheckCall(array_call, **kwargs):
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14 """
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15 This class handle exceptions and call the tool.
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16 It maps the signature of subprocess.check_call:
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17 See https://docs.python.org/2/library/subprocess.html#subprocess.check_call
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18 """
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19 stdin = kwargs.get('stdin')
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20 stdout = kwargs.get('stdout')
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21 stderr = kwargs.get('stderr')
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22 shell = kwargs.get('shell')
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23 try:
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24 p = subprocess.check_call(array_call, stdin=stdin, stdout=stdout, stderr=stderr, shell=shell)
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25 except subprocess.CalledProcessError:
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26 raise
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27 return p
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30 def twoBitInfo(two_bit_file_name, two_bit_info_file):
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31 """
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32 Call twoBitInfo and write the result into twoBit_info_file
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33 :param two_bit_file_name:
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34 :param two_bit_info_file:
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35 :return the subprocess.check_call return object:
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36 """
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37 array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
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38 p = _handleExceptionAndCheckCall(array_call)
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39 return p
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41
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42 def faToTwoBit(fasta_file_name, mySpecieFolder):
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43 """
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44 This function call faToTwoBit UCSC tool, and return the twoBitFile
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45 :param fasta_file_name:
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46 :param mySpecieFolder:
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47 :return:
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48 """
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49 baseNameFasta = os.path.basename(fasta_file_name)
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50 suffixTwoBit, extensionTwoBit = os.path.splitext(baseNameFasta)
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51 nameTwoBit = suffixTwoBit + '.2bit'
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52
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53 with open(os.path.join(mySpecieFolder, nameTwoBit), 'w') as twoBitFile:
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54 array_call = ['faToTwoBit', fasta_file_name, twoBitFile.name]
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55 _handleExceptionAndCheckCall(array_call)
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56
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57 return twoBitFile
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58
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59
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60 def gtfToGenePred(input_gtf_file_name, gene_pred_file_name):
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61 """
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62 Call gtfToGenePred and write the result into gene_pred_file_name
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63 :param input_gtf_file_name:
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64 :param gene_pred_file_name:
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65 :return:
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66 """
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67 array_call = ['gtfToGenePred', input_gtf_file_name, gene_pred_file_name]
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68 p = _handleExceptionAndCheckCall(array_call)
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69 return p
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70
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71
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72 def gff3ToGenePred(input_gff3_file_name, gene_pred_file_name):
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73 """
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74 Call gff3ToGenePred and write the result into gene_pred_file_name
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75 :param input_gff3_file_name:
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76 :param gene_pred_file_name:
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77 :return:
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78 """
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79 array_call = ['gff3ToGenePred', input_gff3_file_name, gene_pred_file_name]
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80 p = _handleExceptionAndCheckCall(array_call)
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81 return p
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82
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83
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84 def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):
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85 """
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86 Call genePredToBed and write the result into unsorted_bed_file_name
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87 :param gene_pred_file_name:
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88 :param unsorted_bed_file_name:
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89 :return:
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90 """
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91 array_call = ['genePredToBed', gene_pred_file_name, unsorted_bed_file_name]
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92 p = _handleExceptionAndCheckCall(array_call)
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93 return p
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94
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95
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96 def sort(unsorted_bed_file_name, sorted_bed_file_name):
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97 """
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98 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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99 :param unsorted_bed_file_name:
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100 :param sorted_bed_file_name:
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101 :return:
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102 """
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103 array_call = ['sort', '-k', '1,1', '-k', '2,2n', unsorted_bed_file_name, '-o', sorted_bed_file_name]
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104 p = _handleExceptionAndCheckCall(array_call)
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105 return p
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106
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107
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108 def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
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109 """
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110 Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
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111 :param two_bit_info_file_name:
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112 :param chrom_sizes_file_name:
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113 :return:
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114 """
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115 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
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116 p = _handleExceptionAndCheckCall(array_call)
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117 return p
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118
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119
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120 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name, typeOption=None, autoSql=None):
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121 """
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122 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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123 :param sorted_bed_file_name:
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124 :param chrom_sizes_file_name:
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125 :param big_bed_file_name:
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126 :return:
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127 """
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128 array_call = ['bedToBigBed', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]
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129 if typeOption:
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130 array_call.append(typeOption)
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131 if autoSql:
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132 array_call.append(autoSql)
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133
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134 p = _handleExceptionAndCheckCall(array_call)
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135 return p
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136
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137
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138 def sortBam(input_bam_file_name, output_sorted_bam_name):
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139 """
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140 Call samtools on input_bam_file_name and output the result in output_sorted_bam_name
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141 :param input_bam_file_name:
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142 :param output_sorted_bam_name:
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143 :return:
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144 """
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145 array_call = ['samtools', 'sort', input_bam_file_name, '-o', output_sorted_bam_name]
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146 p = _handleExceptionAndCheckCall(array_call)
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147 return p
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148
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149
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150 def createBamIndex(input_sorted_bam_file_name, output_name_index_name):
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151 """
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152 Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name
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153 :param input_sorted_bam_file_name:
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154 :param output_name_index_name:
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155 :return:
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156 """
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157 array_call = ['samtools', 'index', input_sorted_bam_file_name, output_name_index_name]
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158 p = _handleExceptionAndCheckCall(array_call)
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159 return p