Mercurial > repos > devteam > fastqc
annotate rgFastQC.py @ 8:06819360a9e2 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
| author | devteam |
|---|---|
| date | Mon, 31 Oct 2016 10:40:12 -0400 |
| parents | 3fdc1a74d866 |
| children | 3a458e268066 |
| rev | line source |
|---|---|
| 0 | 1 """ |
| 1 | 2 Rewrite of rgFastQC.py for Version 0.11.2 of FastQC. |
| 3 | |
| 4 Changes implemented from tmcgowan at | |
| 5 https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc | |
| 6 and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc | |
| 7 with minor changes and bug fixes | |
| 0 | 8 |
| 1 | 9 SYNOPSIS |
| 10 | |
| 11 rgFastQC.py -i input_file -j input_file.name -o output_html_file [-d output_directory] | |
| 12 [-f fastq|bam|sam] [-n job_name] [-c contaminant_file] [-e fastqc_executable] | |
| 0 | 13 |
| 1 | 14 EXAMPLE (generated by Galaxy) |
| 0 | 15 |
| 1 | 16 rgFastQC.py -i path/dataset_1.dat -j 1000gsample.fastq -o path/dataset_3.dat -d path/job_working_directory/subfolder |
| 17 -f fastq -n FastQC -c path/dataset_2.dat -e fastqc | |
| 0 | 18 |
| 19 """ | |
| 1 | 20 |
| 0 | 21 import re |
| 22 import os | |
| 1 | 23 import shutil |
| 0 | 24 import subprocess |
| 25 import optparse | |
| 26 import tempfile | |
| 1 | 27 import glob |
| 28 import gzip | |
| 29 import bz2 | |
| 0 | 30 import zipfile |
| 31 | |
| 1 | 32 class FastQCRunner(object): |
|
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06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
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33 |
| 0 | 34 def __init__(self,opts=None): |
| 1 | 35 ''' |
| 36 Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc() | |
| 37 ''' | |
|
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06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
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38 |
| 1 | 39 # Check whether the options are specified and saves them into the object |
| 40 assert opts != None | |
| 41 self.opts = opts | |
| 0 | 42 |
| 1 | 43 def prepare_command_line(self): |
| 44 ''' | |
| 45 Develops the Commandline to run FastQC in Galaxy | |
| 46 ''' | |
|
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06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
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47 |
| 1 | 48 # Check whether a given file compression format is valid |
| 49 # This prevents uncompression of already uncompressed files | |
| 0 | 50 infname = self.opts.inputfilename |
| 51 linf = infname.lower() | |
| 52 trimext = False | |
| 53 # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf | |
| 54 # patched may 29 2013 until this is fixed properly | |
|
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06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
55 if ( linf.endswith('.gz') or linf.endswith('.gzip') ): |
| 0 | 56 f = gzip.open(self.opts.input) |
| 57 try: | |
| 1 | 58 f.readline() |
| 0 | 59 except: |
| 60 trimext = True | |
| 61 f.close() | |
| 62 elif linf.endswith('bz2'): | |
| 63 f = bz2.open(self.opts.input,'rb') | |
| 64 try: | |
| 65 f.readline() | |
| 66 except: | |
| 67 trimext = True | |
| 68 f.close() | |
| 69 elif linf.endswith('.zip'): | |
| 70 if not zipfile.is_zipfile(self.opts.input): | |
| 71 trimext = True | |
| 72 if trimext: | |
| 1 | 73 f = open(self.opts.input) |
| 74 try: | |
| 75 f.readline() | |
| 76 except: | |
| 77 raise Exception("Input file corruption, could not identify the filetype") | |
| 78 infname = os.path.splitext(infname)[0] | |
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06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
79 |
| 1 | 80 # Replace unwanted or problematic charaters in the input file name |
| 81 self.fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname)) | |
| 4 | 82 # check that the symbolic link gets a proper ending, fastqc seems to ignore the given format otherwise |
| 83 if 'fastq' in opts.informat: | |
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8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
84 # with fastq the .ext is ignored, but when a format is actually passed it must comply with fastqc's |
| 4 | 85 # accepted formats.. |
| 86 opts.informat = 'fastq' | |
| 87 elif not self.fastqinfilename.endswith(opts.informat): | |
| 88 self.fastqinfilename += '.%s' % opts.informat | |
| 89 | |
| 1 | 90 # Build the Commandline from the given parameters |
| 91 command_line = [opts.executable, '--outdir %s' % opts.outputdir] | |
| 92 if opts.contaminants != None: | |
| 93 command_line.append('--contaminants %s' % opts.contaminants) | |
| 94 if opts.limits != None: | |
| 95 command_line.append('--limits %s' % opts.limits) | |
| 96 command_line.append('--quiet') | |
| 97 command_line.append('--extract') # to access the output text file | |
| 98 command_line.append(self.fastqinfilename) | |
| 4 | 99 command_line.append('-f %s' % opts.informat) |
| 1 | 100 self.command_line = ' '.join(command_line) |
| 101 | |
| 102 def copy_output_file_to_dataset(self): | |
| 103 ''' | |
| 104 Retrieves the output html and text files from the output directory and copies them to the Galaxy output files | |
| 105 ''' | |
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8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
106 |
| 1 | 107 # retrieve html file |
| 108 result_file = glob.glob(opts.outputdir + '/*html') | |
| 109 with open(result_file[0], 'rb') as fsrc: | |
| 110 with open(self.opts.htmloutput, 'wb') as fdest: | |
| 111 shutil.copyfileobj(fsrc, fdest) | |
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8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
112 |
| 1 | 113 # retrieve text file |
| 114 text_file = glob.glob(opts.outputdir + '/*/fastqc_data.txt') | |
| 115 with open(text_file[0], 'rb') as fsrc: | |
| 116 with open(self.opts.textoutput, 'wb') as fdest: | |
| 117 shutil.copyfileobj(fsrc, fdest) | |
| 118 | |
| 119 def run_fastqc(self): | |
| 120 ''' | |
| 121 Executes FastQC. Make sure the mandatory import parameters input, inputfilename, outputdir and htmloutput have been specified in the options (opts) | |
| 122 ''' | |
|
8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
123 |
| 1 | 124 # Create a log file |
| 125 dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir) | |
| 126 sout = open(tlog, 'w') | |
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8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
127 |
| 1 | 128 self.prepare_command_line() |
| 129 sout.write(self.command_line) | |
| 130 sout.write('\n') | |
| 131 sout.write("Creating symlink\n") # between the input (.dat) file and the given input file name | |
| 132 os.symlink(self.opts.input, self.fastqinfilename) | |
| 133 sout.write("check_call\n") | |
| 134 subprocess.check_call(self.command_line, shell=True) | |
| 135 sout.write("Copying working %s file to %s \n" % (self.fastqinfilename, self.opts.htmloutput)) | |
| 136 self.copy_output_file_to_dataset() | |
| 137 sout.write("Finished") | |
| 0 | 138 sout.close() |
| 139 | |
| 140 if __name__ == '__main__': | |
| 141 op = optparse.OptionParser() | |
| 142 op.add_option('-i', '--input', default=None) | |
| 1 | 143 op.add_option('-j', '--inputfilename', default=None) |
| 0 | 144 op.add_option('-o', '--htmloutput', default=None) |
| 1 | 145 op.add_option('-t', '--textoutput', default=None) |
| 0 | 146 op.add_option('-d', '--outputdir', default="/tmp/shortread") |
| 147 op.add_option('-f', '--informat', default='fastq') | |
| 148 op.add_option('-n', '--namejob', default='rgFastQC') | |
| 149 op.add_option('-c', '--contaminants', default=None) | |
| 1 | 150 op.add_option('-l', '--limits', default=None) |
| 0 | 151 op.add_option('-e', '--executable', default='fastqc') |
| 152 opts, args = op.parse_args() | |
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8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
153 |
| 1 | 154 assert opts.input != None |
| 155 assert opts.inputfilename != None | |
| 156 assert opts.htmloutput != None | |
|
8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
157 if not os.path.exists(opts.outputdir): |
| 0 | 158 os.makedirs(opts.outputdir) |
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8
06819360a9e2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc commit df4c0b0c6372e2984966e220fa42ecd8a3d370e8
devteam
parents:
7
diff
changeset
|
159 |
| 1 | 160 fastqc_runner = FastQCRunner(opts) |
| 3 | 161 fastqc_runner.run_fastqc() |