Mercurial > repos > devteam > fastqc

annotate rgFastQC.py @ 11:db2dc6bc8f05 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 168f7aeb0f9f38de6dec873f3cbf0c30014fdd72
author iuc
date Thu, 20 Apr 2017 11:06:17 -0400
parents a00a6402d09a
children f2e8552cf1d0
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1 """
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2 Rewrite of rgFastQC.py for Version 0.11.2 of FastQC.
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3
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4 Changes implemented from tmcgowan at
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5 https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc
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6 and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc
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7 with minor changes and bug fixes
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8
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9 SYNOPSIS
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10
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11 rgFastQC.py -i input_file -j input_file.name -o output_html_file [-d output_directory]
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12 [-f fastq|bam|sam] [-n job_name] [-c contaminant_file] [-e fastqc_executable]
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13
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14 EXAMPLE (generated by Galaxy)
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15
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16 rgFastQC.py -i path/dataset_1.dat -j 1000gsample.fastq -o path/dataset_3.dat -d path/job_working_directory/subfolder
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17 -f fastq -n FastQC -c path/dataset_2.dat -e fastqc
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18 """
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19 import bz2
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20 import glob
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21 import gzip
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22 import mimetypes
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23 import optparse
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24 import os
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25 import re
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26 import shutil
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27 import subprocess
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28 import tempfile
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29 import zipfile
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31
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32 class FastQCRunner(object):
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33 def __init__(self, opts=None):
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34 '''
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35 Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc()
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36 '''
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37
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38 # Check whether the options are specified and saves them into the object
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39 assert opts is not None
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40 self.opts = opts
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41
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42 def prepare_command_line(self):
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43 '''
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44 Develops the Commandline to run FastQC in Galaxy
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45 '''
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46
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47 # Check whether a given file compression format is valid
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48 # This prevents uncompression of already uncompressed files
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49 infname = self.opts.inputfilename
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50 linf = infname.lower()
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51 informat = self.opts.informat
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52 trimext = False
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53 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
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54 # patched may 29 2013 until this is fixed properly
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55 ftype = mimetypes.guess_type(self.opts.input)
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56 if linf.endswith('.gz') or linf.endswith('.gzip') or ftype[-1] == "gzip" or informat.endswith('.gz'):
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57 f = gzip.open(self.opts.input)
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58 try:
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59 f.readline()
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60 ftype = ['gzip']
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61 except:
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62 trimext = True
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63 f.close()
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64 elif linf.endswith('bz2') or informat.endswith('.bz2'):
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65 f = bz2.BZ2File(self.opts.input, 'r')
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66 try:
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67 ftype = ['bzip2']
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68 f.readline()
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69 except:
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70 trimext = True
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71 f.close()
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72 elif linf.endswith('.zip'):
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73 if not zipfile.is_zipfile(self.opts.input):
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74 trimext = True
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75 if trimext:
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76 f = open(self.opts.input)
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77 try:
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78 f.readline()
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79 except:
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80 raise Exception("Input file corruption, could not identify the filetype")
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81 infname = os.path.splitext(infname)[0]
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82
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83 # Replace unwanted or problematic charaters in the input file name
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84 self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
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85 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
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86 if 'fastq' in self.opts.informat:
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87 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
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88 # accepted formats..
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89 self.opts.informat = 'fastq'
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90 elif not self.fastqinfilename.endswith(self.opts.informat):
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91 self.fastqinfilename += '.%s' % self.opts.informat
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92
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93 # Build the Commandline from the given parameters
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94 command_line = [opts.executable, '--outdir %s' % self.opts.outputdir]
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95 if self.opts.contaminants is not None:
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96 command_line.append('--contaminants %s' % self.opts.contaminants)
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97 if self.opts.limits is not None:
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98 command_line.append('--limits %s' % self.opts.limits)
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99 command_line.append('--quiet')
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100 command_line.append('--extract') # to access the output text file
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101 if ftype[-1] == 'gzip':
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102 self.fastqinfilename += '.gz'
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103 elif ftype[-1] == 'bzip2':
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104 self.fastqinfilename += '.bz2'
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105 else:
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106 command_line.append('-f %s' % self.opts.informat)
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107 command_line.append(self.fastqinfilename)
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108 self.command_line = ' '.join(command_line)
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109
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110 def copy_output_file_to_dataset(self):
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111 '''
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112 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files
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113 '''
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114
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115 # retrieve html file
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116 result_file = glob.glob(self.opts.outputdir + '/*html')
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117 with open(result_file[0], 'rb') as fsrc:
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118 with open(self.opts.htmloutput, 'wb') as fdest:
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119 shutil.copyfileobj(fsrc, fdest)
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120
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121 # retrieve text file
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122 text_file = glob.glob(self.opts.outputdir + '/*/fastqc_data.txt')
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123 with open(text_file[0], 'rb') as fsrc:
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124 with open(self.opts.textoutput, 'wb') as fdest:
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125 shutil.copyfileobj(fsrc, fdest)
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126
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127 def run_fastqc(self):
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128 '''
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129 Executes FastQC. Make sure the mandatory import parameters input, inputfilename, outputdir and htmloutput have been specified in the options
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130 '''
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131
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132 # Create a log file
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133 dummy, tlog = tempfile.mkstemp(prefix='rgFastQC', suffix=".log", dir=self.opts.outputdir)
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134 sout = open(tlog, 'w')
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135
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136 self.prepare_command_line()
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137 sout.write(self.command_line)
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138 sout.write('\n')
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139 sout.write("Creating symlink\n") # between the input (.dat) file and the given input file name
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140 os.symlink(self.opts.input, self.fastqinfilename)
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141 sout.write("check_call\n")
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142 subprocess.check_call(self.command_line, shell=True)
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143 sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput))
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144 self.copy_output_file_to_dataset()
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145 sout.write("Finished")
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146 sout.close()
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147
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148
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149 if __name__ == '__main__':
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150 op = optparse.OptionParser()
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151 op.add_option('-i', '--input', default=None)
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152 op.add_option('-j', '--inputfilename', default=None)
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153 op.add_option('-o', '--htmloutput', default=None)
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154 op.add_option('-t', '--textoutput', default=None)
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155 op.add_option('-d', '--outputdir', default="/tmp/shortread")
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156 op.add_option('-f', '--informat', default='fastq')
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157 op.add_option('-n', '--namejob', default='rgFastQC')
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158 op.add_option('-c', '--contaminants', default=None)
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159 op.add_option('-l', '--limits', default=None)
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160 op.add_option('-e', '--executable', default='fastqc')
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161 opts, args = op.parse_args()
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162
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163 assert opts.input is not None
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164 assert opts.inputfilename is not None
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165 assert opts.htmloutput is not None
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166 if not os.path.exists(opts.outputdir):
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167 os.makedirs(opts.outputdir)
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168
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169 fastqc_runner = FastQCRunner(opts)
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170 fastqc_runner.run_fastqc()