--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgFastQC.py	Sat Jan 18 22:33:24 2014 -0500
@@ -0,0 +1,233 @@
+"""
+# May 2013 ross added check for bogus gz extension - fastqc gets confused
+# added sanitizer for user supplied name
+# removed shell and make cl a sequence for Popen call
+# ross lazarus August 10 2012 in response to anon insecurity report
+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 re
+import os
+import sys
+import subprocess
+import optparse
+import shutil
+import tempfile
+import zipfile
+import gzip
+
+def pathfind(program):
+    """ toolshed path munging isn't so try to work around june 5 2013
+    """
+    def is_exe(fpath):
+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+    fpath, fname = os.path.split(program)
+    if fpath:
+        if is_exe(program):
+            return program
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            path = path.strip('"')
+            exe_file = os.path.join(path, program)
+            if is_exe(exe_file):
+                return exe_file
+
+    return None    
+
+class FastQC():
+    """wrapper
+    """
+    
+    
+    def __init__(self,opts=None):
+        assert opts <> None
+        self.opts = opts
+        fastqcexe = pathfind(opts.executable)
+        assert (fastqcexe != None),'##rgFastQC.py error - cannot find passed fastqc executable %s in path %s' % (opts.executable,os.environ['PATH'])
+        self.fastqcexe = fastqcexe
+        
+    def getFileString(self, fpath, outpath):
+        """
+        format a nice file size string
+        """
+        size = ''
+        fp = os.path.join(outpath, fpath)
+        s = fpath
+        if os.path.isfile(fp):
+            n = float(os.path.getsize(fp))
+            if n > 2**20:
+                size = ' (%1.1f MB)' % (n/2**20)
+            elif n > 2**10:
+                size = ' (%1.1f KB)' % (n/2**10)
+            elif n > 0:
+                size = ' (%d B)' % (int(n))
+        s = '%s %s' % (fpath, size)
+        return s
+
+    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
+
+        """
+        serr = ''
+        dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir)
+        sout = open(tlog, 'w')
+        fastq = os.path.basename(self.opts.input)
+        cl = [self.fastqcexe,'--outdir=%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('--contaminants=%s' % self.opts.contaminants)
+        # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30
+        # use a symlink in a temporary directory so that the FastQC report reflects the history input file name
+        # note this exposes a bug in the EBI_SRA download tool which leaves bogus .gz extensions on uncompressed files
+        # which fastqc helpfully tries to uncompress again - hilarity ensues.
+        # patched may 29 2013 until this is fixed properly
+        infname = self.opts.inputfilename
+        linf = infname.lower()
+        trimext = False
+        if ( linf.endswith('.gz') or linf.endswith('.gzip') ): 
+            f = gzip.open(self.opts.input)
+            try:
+               testrow = f.readline()
+            except:
+               trimext = True
+            f.close()
+        elif linf.endswith('bz2'):
+           f = bz2.open(self.opts.input,'rb')
+           try:
+              f.readline()
+           except:
+              trimext = True
+           f.close()
+        elif linf.endswith('.zip'):
+           if not zipfile.is_zipfile(self.opts.input):
+              trimext = True
+        if trimext:
+           infname = os.path.splitext(infname)[0]
+        fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(infname))
+        link_name = os.path.join(self.opts.outputdir, fastqinfilename)
+        os.symlink(self.opts.input, link_name)
+        cl.append(link_name)        
+        sout.write('# FastQC cl = %s\n' % ' '.join(cl))
+        sout.flush()
+        p = subprocess.Popen(cl, shell=False, stderr=sout, stdout=sout, cwd=self.opts.outputdir)
+        retval = p.wait()
+        sout.close()
+        runlog = open(tlog,'r').readlines()
+        os.unlink(link_name)
+        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:
+            serr = '\n'.join(runlog)       
+            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,1,serr
+        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,retval,serr
+        
+
+        
+    def fix_fastqc(self,rep=[],flist=[],runlog=[]):
+        """ add some of our stuff to the html
+        """
+        bodyindex = len(rep) -1  # hope they don't change this
+        footrow = bodyindex - 1 
+        footer = rep[footrow]
+        rep = rep[:footrow] + rep[footrow+1:]
+        res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\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,self.getFileString(fn, self.opts.outputdir)))
+        res.append('</table>\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</div>')
+        res.append(footer)
+        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('-j', '--inputfilename', 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
+    if not os.path.exists(opts.outputdir): 
+        os.makedirs(opts.outputdir)
+    f = FastQC(opts)
+    html,retval,serr = f.run_fastqc()
+    f = open(opts.htmloutput, 'w')
+    f.write(''.join(html))
+    f.close()
+    if retval <> 0:
+         print >> sys.stderr, serr # indicate failure
+         
+    
+