Mercurial > repos > xuebing > sharplabtool
diff tools/rgenetics/rgFastQC.py @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rgenetics/rgFastQC.py Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,149 @@ +""" +wrapper for fastqc + +called as + <command interpreter="python"> + rgFastqc.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" + </command> + + + +Current release seems overly intolerant of sam/bam header strangeness +Author notified... + + +""" + +import os,sys,subprocess,optparse,shutil,tempfile +from rgutils import getFileString + +class FastQC(): + """wrapper + """ + + + def __init__(self,opts=None): + assert opts <> None + self.opts = opts + + + def run_fastqc(self): + """ + In batch mode fastqc behaves not very nicely - will write to a new folder in + the same place as the infile called [infilebasename]_fastqc + rlazarus@omics:/data/galaxy/test$ ls FC041_1_sequence_fastqc + duplication_levels.png fastqc_icon.png per_base_n_content.png per_sequence_gc_content.png summary.txt + error.png fastqc_report.html per_base_quality.png per_sequence_quality.png tick.png + fastqc_data.txt per_base_gc_content.png per_base_sequence_content.png sequence_length_distribution.png warning.png + + """ + dummy,tlog = tempfile.mkstemp(prefix='rgFastQClog') + sout = open(tlog, 'w') + fastq = os.path.basename(self.opts.input) + cl = [self.opts.executable,'-o %s' % self.opts.outputdir] + if self.opts.informat in ['sam','bam']: + cl.append('-f %s' % self.opts.informat) + if self.opts.contaminants <> None : + cl.append('-c %s' % self.opts.contaminants) + cl.append(self.opts.input) + p = subprocess.Popen(' '.join(cl), shell=True, stderr=sout, stdout=sout, cwd=self.opts.outputdir) + return_value = p.wait() + sout.close() + runlog = open(tlog,'r').readlines() + os.unlink(tlog) + flist = os.listdir(self.opts.outputdir) # fastqc plays games with its output directory name. eesh + odpath = None + for f in flist: + d = os.path.join(self.opts.outputdir,f) + if os.path.isdir(d): + if d.endswith('_fastqc'): + odpath = d + hpath = None + if odpath <> None: + try: + hpath = os.path.join(odpath,'fastqc_report.html') + rep = open(hpath,'r').readlines() # for our new html file but we need to insert our stuff after the <body> tag + except: + pass + if hpath == None: + res = ['## odpath=%s: No output found in %s. Output for the run was:<pre>\n' % (odpath,hpath),] + res += runlog + res += ['</pre>\n', + 'Please read the above for clues<br/>\n', + 'If you selected a sam/bam format file, it might not have headers or they may not start with @HD?<br/>\n', + 'It is also possible that the log shows that fastqc is not installed?<br/>\n', + 'If that is the case, please tell the relevant Galaxy administrator that it can be snarfed from<br/>\n', + 'http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/<br/>\n',] + return res + self.fix_fastqcimages(odpath) + flist = os.listdir(self.opts.outputdir) # these have now been fixed + excludefiles = ['tick.png','warning.png','fastqc_icon.png','error.png'] + flist = [x for x in flist if not x in excludefiles] + for i in range(len(rep)): # need to fix links to Icons and Image subdirectories in lastest fastqc code - ugh + rep[i] = rep[i].replace('Icons/','') + rep[i] = rep[i].replace('Images/','') + + html = self.fix_fastqc(rep,flist,runlog) + return html + + + + def fix_fastqc(self,rep=[],flist=[],runlog=[]): + """ add some of our stuff to the html + """ + bs = '</body></html>\n' # hope they don't change this + try: + bodyindex = rep.index(bs) # hope they don't change this + except: + bodyindex = len(rep) - 1 + res = [] + res.append('<table>\n') + flist.sort() + for i,f in enumerate(flist): + if not(os.path.isdir(f)): + fn = os.path.split(f)[-1] + res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir))) + res.append('</table><p/>\n') + res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n') + res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n') + fixed = rep[:bodyindex] + res + rep[bodyindex:] + return fixed # with our additions + + + def fix_fastqcimages(self,odpath): + """ Galaxy wants everything in the same files_dir + """ + icpath = os.path.join(odpath,'Icons') + impath = os.path.join(odpath,'Images') + for adir in [icpath,impath,odpath]: + if os.path.exists(adir): + flist = os.listdir(adir) # get all files created + for f in flist: + if not os.path.isdir(os.path.join(adir,f)): + sauce = os.path.join(adir,f) + dest = os.path.join(self.opts.outputdir,f) + shutil.move(sauce,dest) + os.rmdir(adir) + + + +if __name__ == '__main__': + op = optparse.OptionParser() + op.add_option('-i', '--input', default=None) + op.add_option('-o', '--htmloutput', default=None) + op.add_option('-d', '--outputdir', default="/tmp/shortread") + op.add_option('-f', '--informat', default='fastq') + op.add_option('-n', '--namejob', default='rgFastQC') + op.add_option('-c', '--contaminants', default=None) + op.add_option('-e', '--executable', default='fastqc') + opts, args = op.parse_args() + assert opts.input <> None + assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable + if not os.path.exists(opts.outputdir): + os.makedirs(opts.outputdir) + f = FastQC(opts) + html = f.run_fastqc() + f = open(opts.htmloutput, 'w') + f.write(''.join(html)) + f.close() +