Mercurial > repos > cstrittmatter > test_galtrakr_eurl_vtec_wgs_pt_23

annotate scripts/rgFastQC.py @ 1:5224b4d51065 tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit cb65588391944306ff3cb32a23e1c28f65122014-dirty"
author cstrittmatter
date Fri, 11 Mar 2022 15:52:43 -0500
parents 8be2feb96994
children
rev   line source
cstrittmatter@0 1 """
cstrittmatter@0 2 Rewrite of rgFastQC.py for Version 0.11.2 of FastQC.
cstrittmatter@0 3
cstrittmatter@0 4 Changes implemented from tmcgowan at
cstrittmatter@0 5 https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc
cstrittmatter@0 6 and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc
cstrittmatter@0 7 with minor changes and bug fixes
cstrittmatter@0 8
cstrittmatter@0 9 SYNOPSIS
cstrittmatter@0 10
cstrittmatter@0 11 rgFastQC.py -i input_file -j input_file.name -o output_html_file [-d output_directory]
cstrittmatter@0 12 [-f fastq|bam|sam] [-n job_name] [-c contaminant_file] [-e fastqc_executable]
cstrittmatter@0 13
cstrittmatter@0 14 EXAMPLE (generated by Galaxy)
cstrittmatter@0 15
cstrittmatter@0 16 rgFastQC.py -i path/dataset_1.dat -j 1000gsample.fastq -o path/dataset_3.dat -d path/job_working_directory/subfolder
cstrittmatter@0 17 -f fastq -n FastQC -c path/dataset_2.dat -e fastqc
cstrittmatter@0 18
cstrittmatter@0 19 """
cstrittmatter@0 20
cstrittmatter@0 21 import re
cstrittmatter@0 22 import os
cstrittmatter@0 23 import shutil
cstrittmatter@0 24 import subprocess
cstrittmatter@0 25 import optparse
cstrittmatter@0 26 import tempfile
cstrittmatter@0 27 import glob
cstrittmatter@0 28 import gzip
cstrittmatter@0 29 import bz2
cstrittmatter@0 30 import zipfile
cstrittmatter@0 31
cstrittmatter@0 32 class FastQCRunner(object):
cstrittmatter@0 33
cstrittmatter@0 34 def __init__(self,opts=None):
cstrittmatter@0 35 '''
cstrittmatter@0 36 Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc()
cstrittmatter@0 37 '''
cstrittmatter@0 38
cstrittmatter@0 39 # Check whether the options are specified and saves them into the object
cstrittmatter@0 40 assert opts != None
cstrittmatter@0 41 self.opts = opts
cstrittmatter@0 42
cstrittmatter@0 43 def prepare_command_line(self):
cstrittmatter@0 44 '''
cstrittmatter@0 45 Develops the Commandline to run FastQC in Galaxy
cstrittmatter@0 46 '''
cstrittmatter@0 47
cstrittmatter@0 48 # Check whether a given file compression format is valid
cstrittmatter@0 49 # This prevents uncompression of already uncompressed files
cstrittmatter@0 50 infname = self.opts.inputfilename
cstrittmatter@0 51 linf = infname.lower()
cstrittmatter@0 52 trimext = False
cstrittmatter@0 53 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf
cstrittmatter@0 54 # patched may 29 2013 until this is fixed properly
cstrittmatter@0 55 if ( linf.endswith('.gz') or linf.endswith('.gzip') ):
cstrittmatter@0 56 f = gzip.open(self.opts.input)
cstrittmatter@0 57 try:
cstrittmatter@0 58 f.readline()
cstrittmatter@0 59 except:
cstrittmatter@0 60 trimext = True
cstrittmatter@0 61 f.close()
cstrittmatter@0 62 elif linf.endswith('bz2'):
cstrittmatter@0 63 f = bz2.open(self.opts.input,'rb')
cstrittmatter@0 64 try:
cstrittmatter@0 65 f.readline()
cstrittmatter@0 66 except:
cstrittmatter@0 67 trimext = True
cstrittmatter@0 68 f.close()
cstrittmatter@0 69 elif linf.endswith('.zip'):
cstrittmatter@0 70 if not zipfile.is_zipfile(self.opts.input):
cstrittmatter@0 71 trimext = True
cstrittmatter@0 72 if trimext:
cstrittmatter@0 73 f = open(self.opts.input)
cstrittmatter@0 74 try:
cstrittmatter@0 75 f.readline()
cstrittmatter@0 76 except:
cstrittmatter@0 77 raise Exception("Input file corruption, could not identify the filetype")
cstrittmatter@0 78 infname = os.path.splitext(infname)[0]
cstrittmatter@0 79
cstrittmatter@0 80 # Replace unwanted or problematic charaters in the input file name
cstrittmatter@0 81 self.fastqinfilename = re.sub(r'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
cstrittmatter@0 82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise
cstrittmatter@0 83 if 'fastq' in opts.informat:
cstrittmatter@0 84 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's
cstrittmatter@0 85 # accepted formats..
cstrittmatter@0 86 opts.informat = 'fastq'
cstrittmatter@0 87 elif not self.fastqinfilename.endswith(opts.informat):
cstrittmatter@0 88 self.fastqinfilename += '.%s' % opts.informat
cstrittmatter@0 89
cstrittmatter@0 90 # Build the Commandline from the given parameters
cstrittmatter@0 91 command_line = [opts.executable, '--outdir %s' % opts.outputdir]
cstrittmatter@0 92 if opts.contaminants != None:
cstrittmatter@0 93 command_line.append('--contaminants %s' % opts.contaminants)
cstrittmatter@0 94 if opts.limits != None:
cstrittmatter@0 95 command_line.append('--limits %s' % opts.limits)
cstrittmatter@0 96 command_line.append('--quiet')
cstrittmatter@0 97 command_line.append('--extract') # to access the output text file
cstrittmatter@0 98 command_line.append(self.fastqinfilename)
cstrittmatter@0 99 command_line.append('-f %s' % opts.informat)
cstrittmatter@0 100 self.command_line = ' '.join(command_line)
cstrittmatter@0 101
cstrittmatter@0 102 def copy_output_file_to_dataset(self):
cstrittmatter@0 103 '''
cstrittmatter@0 104 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files
cstrittmatter@0 105 '''
cstrittmatter@0 106
cstrittmatter@0 107 # retrieve html file
cstrittmatter@0 108 result_file = glob.glob(opts.outputdir + '/*html')
cstrittmatter@0 109 with open(result_file[0], 'rb') as fsrc:
cstrittmatter@0 110 with open(self.opts.htmloutput, 'wb') as fdest:
cstrittmatter@0 111 shutil.copyfileobj(fsrc, fdest)
cstrittmatter@0 112
cstrittmatter@0 113 # retrieve text file
cstrittmatter@0 114 text_file = glob.glob(opts.outputdir + '/*/fastqc_data.txt')
cstrittmatter@0 115 with open(text_file[0], 'rb') as fsrc:
cstrittmatter@0 116 with open(self.opts.textoutput, 'wb') as fdest:
cstrittmatter@0 117 shutil.copyfileobj(fsrc, fdest)
cstrittmatter@0 118
cstrittmatter@0 119 def run_fastqc(self):
cstrittmatter@0 120 '''
cstrittmatter@0 121 Executes FastQC. Make sure the mandatory import parameters input, inputfilename, outputdir and htmloutput have been specified in the options (opts)
cstrittmatter@0 122 '''
cstrittmatter@0 123
cstrittmatter@0 124 # Create a log file
cstrittmatter@0 125 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
cstrittmatter@0 126 sout = open(tlog, 'w')
cstrittmatter@0 127
cstrittmatter@0 128 self.prepare_command_line()
cstrittmatter@0 129 sout.write(self.command_line)
cstrittmatter@0 130 sout.write('\n')
cstrittmatter@0 131 sout.write("Creating symlink\n") # between the input (.dat) file and the given input file name
cstrittmatter@0 132 os.symlink(self.opts.input, self.fastqinfilename)
cstrittmatter@0 133 sout.write("check_call\n")
cstrittmatter@0 134 subprocess.check_call(self.command_line, shell=True)
cstrittmatter@0 135 sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput))
cstrittmatter@0 136 self.copy_output_file_to_dataset()
cstrittmatter@0 137 sout.write("Finished")
cstrittmatter@0 138 sout.close()
cstrittmatter@0 139
cstrittmatter@0 140 if __name__ == '__main__':
cstrittmatter@0 141 op = optparse.OptionParser()
cstrittmatter@0 142 op.add_option('-i', '--input', default=None)
cstrittmatter@0 143 op.add_option('-j', '--inputfilename', default=None)
cstrittmatter@0 144 op.add_option('-o', '--htmloutput', default=None)
cstrittmatter@0 145 op.add_option('-t', '--textoutput', default=None)
cstrittmatter@0 146 op.add_option('-d', '--outputdir', default="/tmp/shortread")
cstrittmatter@0 147 op.add_option('-f', '--informat', default='fastq')
cstrittmatter@0 148 op.add_option('-n', '--namejob', default='rgFastQC')
cstrittmatter@0 149 op.add_option('-c', '--contaminants', default=None)
cstrittmatter@0 150 op.add_option('-l', '--limits', default=None)
cstrittmatter@0 151 op.add_option('-e', '--executable', default='fastqc')
cstrittmatter@0 152 opts, args = op.parse_args()
cstrittmatter@0 153
cstrittmatter@0 154 assert opts.input != None
cstrittmatter@0 155 assert opts.inputfilename != None
cstrittmatter@0 156 assert opts.htmloutput != None
cstrittmatter@0 157 #assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
cstrittmatter@0 158 if not os.path.exists(opts.outputdir):
cstrittmatter@0 159 os.makedirs(opts.outputdir)
cstrittmatter@0 160
cstrittmatter@0 161 fastqc_runner = FastQCRunner(opts)
cstrittmatter@0 162 fastqc_runner.run_fastqc()