Mercurial > repos > jjohnson > fastqc

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:22:05 -0400
parents
children
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0
1d373f219445 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #!/usr/bin/env python
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2
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3 """
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4 Runs FastQC on a fastq file;
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5 TODO: more documentation
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6
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7 usage: fastqc.py [options]
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8 -i, --input=i: The fastq input file
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9 -n, --name=n: The fastq input name
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10 -c, --contaminants=c: A contaminants file
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11 -r, --report=r: The html summary report file
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12 -D, --dir=D: The dir for report files
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13 -d, --data=d: The data output text file
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14 """
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15
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16 import optparse, os, shutil, subprocess, sys, tempfile, re, string
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17
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18 def stop_err( msg ):
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19 sys.stderr.write( '%s\n' % msg )
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20 sys.exit()
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21
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22 def __main__():
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23 #Parse Command Line
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24 parser = optparse.OptionParser()
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25 parser.add_option( '-i', '--input', dest='input', help='The sequence input file' )
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26 parser.add_option( '-f', '--format', dest='format', help='The sequence input file format' )
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27 parser.add_option( '-n', '--name', dest='name', help='The fastq input name' )
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28 parser.add_option( '-c', '--contaminants', dest='contaminants', help='A contaminants file' )
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29 parser.add_option( '-r', '--report', dest='report', help='The HTML report' )
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30 parser.add_option( '-D', '--dir', dest='outdir', help='The dir for report files' )
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31 parser.add_option( '-d', '--data', dest='data', help='The output data text file' )
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32 (options, args) = parser.parse_args()
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33 if options.input == None:
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34 stop_err("Misssing option --input")
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35 params = []
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36 #params.append('-Xmx250m')
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37 params.append('-Djava.awt.headless=true')
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38 name = 'input'
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39 format = 'fastq'
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40 if options.outdir != None:
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41 os.makedirs(options.outdir)
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42 if options.contaminants != None and options.contaminants != 'None':
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43 params.append("-c %s" % options.contaminants)
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44 if options.name != None and options.name != 'None':
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45 name = re.sub('[^a-zA-Z0-9_.-]','_',options.name)
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46 if options.format != None and options.format != 'None':
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47 format = options.format
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48 params.append("-f %s" % options.format)
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49 # FastQC relies on the extension to determine file format .sam .bam or .fastq
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50 if not name.endswith('.'+format):
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51 name = '.'.join((name,format))
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52 # make temp directory
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53 buffsize = 1048576
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54 tmp_dir = tempfile.mkdtemp()
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55 params.append("-o %s" % tmp_dir)
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56 # print("tmp_dir %s" % tmp_dir)
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57 try:
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58 # make a link to the input fastq in the tmp_dir
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59 # FastQC will generate output in the same dir that it finds its input
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60 fastq = os.path.join(tmp_dir,name)
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61 os.symlink( options.input, fastq)
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62 # generate commandline
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63 cmd = 'fastqc %s %s' % (' '.join(params),fastq)
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64 # need to nest try-except in try-finally to handle 2.4
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65 try:
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66 try:
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67 tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
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68 tmp_stderr = open( tmp_stderr_name, 'wb' )
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69 tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name
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70 tmp_stdout = open( tmp_stdout_name, 'wb' )
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71 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() )
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72 returncode = proc.wait()
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73 tmp_stderr.close()
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74 # get stderr, allowing for case where it's very large
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75 tmp_stderr = open( tmp_stderr_name, 'rb' )
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76 stderr = ''
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77 try:
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78 while True:
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79 stderr += tmp_stderr.read( buffsize )
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80 if not stderr or len( stderr ) % buffsize != 0:
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81 break
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82 except OverflowError:
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83 pass
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84 tmp_stderr.close()
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85 if returncode != 0:
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86 raise Exception, stderr
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87 except Exception, e:
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88 raise Exception, 'Error executing FastQC. ' + str( e )
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89 # remove the input file symlink so it does get copied
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90 os.remove(fastq)
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91 # remove the stdout and stderr files so they do not get copied
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92 os.remove(tmp_stderr_name)
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93 os.remove(tmp_stdout_name)
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94 # array to retrieve results of each test so that it gets displayed in the tool info
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95 tests = []
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96 # move result to outdir
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97 # Need to flatten the dir hierachy in order for galaxy to serve the href links
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98 for root, dirs, files in os.walk(tmp_dir):
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99 for fname in files:
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100 path = os.path.join(root,fname)
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101 # print("%s" % fname)
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102 if re.match('.+\.zip',fname):
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103 pass
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104 elif fname == 'fastqc_report.html':
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105 if options.outdir != None:
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106 fsrc = open(path,'r')
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107 # fdst = open(os.path.join(options.outdir,fname),'w')
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108 fdst = open(options.report,'w')
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109 try:
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110 for line in fsrc:
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111 if line.find('footer') > 0:
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112 # add extra links in case someone prefers raw text
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113 fdst.write('<p><a href="summary.txt">FastQC Summary text report</a>')
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114 fdst.write('<p><a href="fastqc_data.txt">FastQC Report Data</a>')
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115 # copy lines removing subdirs from links
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116 fdst.write(re.sub('Icons/|Images/','',line))
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117 finally:
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118 fsrc.close()
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119 fdst.close()
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120 else:
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121 if options.outdir != None:
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122 shutil.copy(path,options.outdir)
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123 if fname == 'summary.txt':
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124 # Use the contents of this file to put stdout info into the HistoryDataset panel
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125 fsrc = open(path,'r')
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126 try:
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127 for line in fsrc:
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128 (grade,test,seq) = string.split(line,' ')
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129 tests.append("%s %s" % ('+' if grade == 'PASS' else '-',re.sub('equence','eq',test)))
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130 finally:
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131 fsrc.close()
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132 elif fname == 'fastqc_data.txt':
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133 if options.data != None:
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134 # copy the fastqc_data.txt file to the dataset data
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135 shutil.copy(path,options.data)
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136 cnt = '?'
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137 flen = '?'
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138 gc = '?'
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139 fsrc = open(path,'r')
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140 try:
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141 for line in fsrc:
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142 m = re.match('^Total Sequences (\d+)',line)
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143 if m:
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144 cnt = m.groups()[-1]
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145 m = re.match('^Sequence length (\d+)',line)
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146 if m:
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147 flen = m.groups()[-1]
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148 m = re.match('^%GC (\d+)',line)
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149 if m:
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150 gc = m.groups()[-1]
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151 finally:
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152 fsrc.close()
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153 #print to stdout so that this appears in the tool dataset info
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154 print("Seqs %s, Len %s, GC %s" %(cnt,flen,gc))
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155 #print to stdout so that this appears in the tool dataset info
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156 print("%s" % '\n'.join(tests))
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157 except Exception, e:
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158 stop_err( 'Fastq failed.\n' + str( e ) )
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159 finally:
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160 # clean up temp dir, put in a try block so we don't fail on stale nfs handles
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161 try:
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162 if os.path.exists( tmp_dir ):
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163 shutil.rmtree( tmp_dir )
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164 except Exception, e:
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165 pass
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166
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167 if __name__=="__main__": __main__()