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1 """
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2 wrapper for fastqc
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3
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4 called as
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5 <command interpreter="python">
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6 rgFastqc.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix"
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7 </command>
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8
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9
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10
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11 Current release seems overly intolerant of sam/bam header strangeness
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12 Author notified...
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13
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14
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15 """
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16
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17 import os,sys,subprocess,optparse,shutil,tempfile
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18 from rgutils import getFileString
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19
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20 class FastQC():
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21 """wrapper
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22 """
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23
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24
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25 def __init__(self,opts=None):
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26 assert opts <> None
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27 self.opts = opts
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28
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29
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30 def run_fastqc(self):
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31 """
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32 In batch mode fastqc behaves not very nicely - will write to a new folder in
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33 the same place as the infile called [infilebasename]_fastqc
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34 rlazarus@omics:/data/galaxy/test$ ls FC041_1_sequence_fastqc
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35 duplication_levels.png fastqc_icon.png per_base_n_content.png per_sequence_gc_content.png summary.txt
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36 error.png fastqc_report.html per_base_quality.png per_sequence_quality.png tick.png
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37 fastqc_data.txt per_base_gc_content.png per_base_sequence_content.png sequence_length_distribution.png warning.png
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38
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39 """
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40 dummy,tlog = tempfile.mkstemp(prefix='rgFastQClog')
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41 sout = open(tlog, 'w')
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42 fastq = os.path.basename(self.opts.input)
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43 cl = [self.opts.executable,'-o %s' % self.opts.outputdir]
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44 if self.opts.informat in ['sam','bam']:
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45 cl.append('-f %s' % self.opts.informat)
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46 if self.opts.contaminants <> None :
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47 cl.append('-c %s' % self.opts.contaminants)
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48 cl.append(self.opts.input)
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49 p = subprocess.Popen(' '.join(cl), shell=True, stderr=sout, stdout=sout, cwd=self.opts.outputdir)
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50 return_value = p.wait()
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51 sout.close()
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52 runlog = open(tlog,'r').readlines()
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53 os.unlink(tlog)
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54 flist = os.listdir(self.opts.outputdir) # fastqc plays games with its output directory name. eesh
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55 odpath = None
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56 for f in flist:
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57 d = os.path.join(self.opts.outputdir,f)
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58 if os.path.isdir(d):
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59 if d.endswith('_fastqc'):
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60 odpath = d
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61 hpath = None
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62 if odpath <> None:
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63 try:
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64 hpath = os.path.join(odpath,'fastqc_report.html')
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65 rep = open(hpath,'r').readlines() # for our new html file but we need to insert our stuff after the <body> tag
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66 except:
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67 pass
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68 if hpath == None:
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69 res = ['## odpath=%s: No output found in %s. Output for the run was:<pre>\n' % (odpath,hpath),]
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70 res += runlog
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71 res += ['</pre>\n',
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72 'Please read the above for clues<br/>\n',
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73 'If you selected a sam/bam format file, it might not have headers or they may not start with @HD?<br/>\n',
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74 'It is also possible that the log shows that fastqc is not installed?<br/>\n',
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75 'If that is the case, please tell the relevant Galaxy administrator that it can be snarfed from<br/>\n',
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76 'http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/<br/>\n',]
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77 return res
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78 self.fix_fastqcimages(odpath)
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79 flist = os.listdir(self.opts.outputdir) # these have now been fixed
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80 excludefiles = ['tick.png','warning.png','fastqc_icon.png','error.png']
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81 flist = [x for x in flist if not x in excludefiles]
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82 for i in range(len(rep)): # need to fix links to Icons and Image subdirectories in lastest fastqc code - ugh
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83 rep[i] = rep[i].replace('Icons/','')
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84 rep[i] = rep[i].replace('Images/','')
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85
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86 html = self.fix_fastqc(rep,flist,runlog)
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87 return html
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88
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89
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90
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91 def fix_fastqc(self,rep=[],flist=[],runlog=[]):
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92 """ add some of our stuff to the html
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93 """
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94 bs = '</body></html>\n' # hope they don't change this
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95 try:
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96 bodyindex = rep.index(bs) # hope they don't change this
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97 except:
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98 bodyindex = len(rep) - 1
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99 res = []
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100 res.append('<table>\n')
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101 flist.sort()
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102 for i,f in enumerate(flist):
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103 if not(os.path.isdir(f)):
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104 fn = os.path.split(f)[-1]
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105 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir)))
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106 res.append('</table><p/>\n')
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107 res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n')
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108 res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n')
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109 fixed = rep[:bodyindex] + res + rep[bodyindex:]
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110 return fixed # with our additions
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111
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112
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113 def fix_fastqcimages(self,odpath):
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114 """ Galaxy wants everything in the same files_dir
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115 """
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116 icpath = os.path.join(odpath,'Icons')
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117 impath = os.path.join(odpath,'Images')
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118 for adir in [icpath,impath,odpath]:
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119 if os.path.exists(adir):
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120 flist = os.listdir(adir) # get all files created
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121 for f in flist:
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122 if not os.path.isdir(os.path.join(adir,f)):
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123 sauce = os.path.join(adir,f)
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124 dest = os.path.join(self.opts.outputdir,f)
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125 shutil.move(sauce,dest)
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126 os.rmdir(adir)
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127
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128
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129
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130 if __name__ == '__main__':
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131 op = optparse.OptionParser()
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132 op.add_option('-i', '--input', default=None)
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133 op.add_option('-o', '--htmloutput', default=None)
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134 op.add_option('-d', '--outputdir', default="/tmp/shortread")
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135 op.add_option('-f', '--informat', default='fastq')
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136 op.add_option('-n', '--namejob', default='rgFastQC')
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137 op.add_option('-c', '--contaminants', default=None)
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138 op.add_option('-e', '--executable', default='fastqc')
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139 opts, args = op.parse_args()
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140 assert opts.input <> None
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141 assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable
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142 if not os.path.exists(opts.outputdir):
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143 os.makedirs(opts.outputdir)
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144 f = FastQC(opts)
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145 html = f.run_fastqc()
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146 f = open(opts.htmloutput, 'w')
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147 f.write(''.join(html))
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148 f.close()
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149
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