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1 #!/usr/bin/env python
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2
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3 '''
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4 FastQC checker for Galaxy biomedical data analysis platform
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5
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6 @author: Ilya Sytchev
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7
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8 Input: one or more files in fastq format
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9 Output: sequencing quality report in text format
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10
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11 Requires FastQC 0.10.0 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/)
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12
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13 Partially based on:
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14 fastqcwrapper (http://toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc)
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15 rgFastQC (https://bitbucket.org/galaxy/galaxy-dist/src/tip/tools/rgenetics/rgFastQC.py)
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16
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17 Tested with Python 2.6.1 and 2.7.2 on Mac OS 10.6.8
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18 '''
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19
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20 import sys, os, optparse, tempfile, shutil, subprocess
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21
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22 def stop_err(msg, returncode=1):
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23 sys.stderr.write(msg)
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24 sys.exit(returncode)
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25
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26 def __main__():
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27 usage = "Usage: %prog -e fastqc_executable -o output_file fastq_file [fastq_file ... ]"
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28 version = "%prog 1.0.0"
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29 op = optparse.OptionParser(usage=usage, version=version)
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30 op.add_option('-e', '--executable', dest="executable", help="location of the FastQC program")
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31 op.add_option('-o', '--output', dest="outfile", help="location of the output file")
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32 (options, infiles) = op.parse_args()
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33
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34 # check if location of the FastQC program was provided
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35 if options.executable == None:
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36 op.error("Missing location of FastQC")
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37
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38 # check if FastQC program exists at the provided location
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39 if not os.path.isfile(options.executable):
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40 op.error("Cannot find FastQC at %s" % options.executable)
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41
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42 # check if any input files were provided
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43 if infiles == None:
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44 op.error("Missing input files")
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45
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46 # check if all input files exist
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47 for f in infiles:
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48 if not os.path.isfile(f):
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49 op.error("Cannot find input file %s" % f)
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50
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51 # check if output file was provided
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52 if options.outfile == None:
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53 op.error("Missing output file name")
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54
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55 # assemble FastQC command line
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56 cmd = [] # list is more secure than string for subprocess call
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57 cmd.append(options.executable)
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58 tmpdir = tempfile.mkdtemp() # create temp dir for FastQC output
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59 cmd.extend(['-o', tmpdir])
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60 cmd.extend(infiles)
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61
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62 # prepare files for FastQC stdout and stderr
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63 tmp_stderr_name = tempfile.NamedTemporaryFile(dir=tmpdir, suffix='.err').name
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64 tmp_stderr = open(tmp_stderr_name, 'w')
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65 tmp_stdout_name = tempfile.NamedTemporaryFile(dir=tmpdir, suffix='.out').name
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66 tmp_stdout = open(tmp_stdout_name, 'w')
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67 # run FastQC
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68 try:
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69 subprocess.check_call(cmd, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno())
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70 except subprocess.CalledProcessError as e:
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71 stop_err("Error executing FastQC\n", e.returncode)
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72 finally:
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73 tmp_stderr.close()
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74 tmp_stdout.close()
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75
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76 outfile = open(options.outfile, 'w')
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77
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78 # parse all summary.txt files produced by FastQC and write results into the output file
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79 for f in infiles:
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80 filename = os.path.basename(f)
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81 (datasetname, extension) = os.path.splitext(filename)
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82 # Need to account for FastQC removing .fastq extension from input file names before using them to create output file and dir names
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83 # Alternative solution is to iterate over report directories instead of input file names
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84 if extension == '.fastq':
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85 summaryfilename = os.path.join(tmpdir, datasetname + '_fastqc', 'summary.txt')
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86 else:
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87 summaryfilename = os.path.join(tmpdir, filename + '_fastqc', 'summary.txt')
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88 outfile.write("%s results:\n" % datasetname)
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89 # if summary file exists, process and add results to the output file
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90 if os.path.isfile(summaryfilename):
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91 summaryfile = open(summaryfilename, 'r')
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92 for line in summaryfile:
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93 (result, test) = line.split('\t')[:2]
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94 outfile.write(result + '\t' + test + '\n')
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95 summaryfile.close()
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96 else:
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97 outfile.write("FastQC summary report was not found at %s.\n" % summaryfilename)
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98 outfile.write("\n")
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99
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100 outfile.close()
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101
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102 # clean up temp dir, put in a try block so we don't fail on stale nfs handles
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103 try:
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104 if os.path.exists(tmpdir):
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105 shutil.rmtree(tmpdir)
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106 except:
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107 pass
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108
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109 if __name__ == '__main__': __main__()
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