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annotate scripts/rgFastQC.py @ 3:0cbed1c0a762 draft default tip

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 965517909457
children
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0
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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 """
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20
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21 import re
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22 import os
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23 import shutil
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24 import subprocess
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25 import optparse
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26 import tempfile
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27 import glob
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28 import gzip
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29 import bz2
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30 import zipfile
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31
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32 class FastQCRunner(object):
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33
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34 def __init__(self,opts=None):
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35 '''
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36 Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc()
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37 '''
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38
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39 # Check whether the options are specified and saves them into the object
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40 assert opts != None
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41 self.opts = opts
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42
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43 def prepare_command_line(self):
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44 '''
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45 Develops the Commandline to run FastQC in Galaxy
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46 '''
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47
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48 # Check whether a given file compression format is valid
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49 # This prevents uncompression of already uncompressed files
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50 infname = self.opts.inputfilename
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51 linf = infname.lower()
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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 if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
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56 f = gzip.open(self.opts.input)
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57 try:
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58 f.readline()
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59 except:
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60 trimext = True
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61 f.close()
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62 elif linf.endswith('bz2'):
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63 f = bz2.open(self.opts.input,'rb')
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64 try:
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65 f.readline()
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66 except:
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67 trimext = True
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68 f.close()
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69 elif linf.endswith('.zip'):
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70 if not zipfile.is_zipfile(self.opts.input):
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71 trimext = True
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72 if trimext:
3
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73 f = open(self.opts.input)
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74 try:
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75 f.readline()
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76 except:
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77 raise Exception("Input file corruption, could not identify the filetype")
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78 infname = os.path.splitext(infname)[0]
0
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79
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80 # Replace unwanted or problematic charaters in the input file name
3
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81 self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
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82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
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83 if 'fastq' in opts.informat:
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84 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
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85 # accepted formats..
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86 opts.informat = 'fastq'
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87 elif not self.fastqinfilename.endswith(opts.informat):
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88 self.fastqinfilename += '.%s' % opts.informat
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89
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90 # Build the Commandline from the given parameters
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91 command_line = [opts.executable, '--outdir %s' % opts.outputdir]
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92 if opts.contaminants != None:
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93 command_line.append('--contaminants %s' % opts.contaminants)
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94 if opts.limits != None:
3
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95 command_line.append('--limits %s' % opts.limits)
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96 command_line.append('--quiet')
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97 command_line.append('--extract') # to access the output text file
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98 command_line.append(self.fastqinfilename)
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99 command_line.append('-f %s' % opts.informat)
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100 self.command_line = ' '.join(command_line)
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101
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102 def copy_output_file_to_dataset(self):
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103 '''
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104 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files
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105 '''
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106
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107 # retrieve html file
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108 result_file = glob.glob(opts.outputdir + '/*html')
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109 with open(result_file[0], 'rb') as fsrc:
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110 with open(self.opts.htmloutput, 'wb') as fdest:
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111 shutil.copyfileobj(fsrc, fdest)
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112
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113 # retrieve text file
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114 text_file = glob.glob(opts.outputdir + '/*/fastqc_data.txt')
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115 with open(text_file[0], 'rb') as fsrc:
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116 with open(self.opts.textoutput, 'wb') as fdest:
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117 shutil.copyfileobj(fsrc, fdest)
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118
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119 def run_fastqc(self):
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120 '''
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121 Executes FastQC. Make sure the mandatory import parameters input, inputfilename, outputdir and htmloutput have been specified in the options (opts)
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122 '''
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123
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124 # Create a log file
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125 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
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126 sout = open(tlog, 'w')
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127
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128 self.prepare_command_line()
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129 sout.write(self.command_line)
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130 sout.write('\n')
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131 sout.write("Creating symlink\n") # between the input (.dat) file and the given input file name
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132 os.symlink(self.opts.input, self.fastqinfilename)
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133 sout.write("check_call\n")
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134 subprocess.check_call(self.command_line, shell=True)
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135 sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput))
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136 self.copy_output_file_to_dataset()
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137 sout.write("Finished")
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138 sout.close()
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139
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140 if __name__ == '__main__':
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141 op = optparse.OptionParser()
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142 op.add_option('-i', '--input', default=None)
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143 op.add_option('-j', '--inputfilename', default=None)
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144 op.add_option('-o', '--htmloutput', default=None)
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145 op.add_option('-t', '--textoutput', default=None)
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146 op.add_option('-d', '--outputdir', default="/tmp/shortread")
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147 op.add_option('-f', '--informat', default='fastq')
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148 op.add_option('-n', '--namejob', default='rgFastQC')
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149 op.add_option('-c', '--contaminants', default=None)
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150 op.add_option('-l', '--limits', default=None)
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151 op.add_option('-e', '--executable', default='fastqc')
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152 opts, args = op.parse_args()
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153
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154 assert opts.input != None
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155 assert opts.inputfilename != None
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156 assert opts.htmloutput != None
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157 #assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
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158 if not os.path.exists(opts.outputdir):
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159 os.makedirs(opts.outputdir)
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160
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161 fastqc_runner = FastQCRunner(opts)
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162 fastqc_runner.run_fastqc()