added a wrapper for weblogo - turns out that there have been lots of errors on main from people trying

to run logos using fasta files containing sequences of variable length. This is a nono but weblogo does not
return a sensible error message. Wrapper checks every sequence length and complains if any variation found
so at least the error message is explicit.

tools/rgenetics/rgWebLogo3.py

@@ -0,0 +1,130 @@
+"""
+# rgWebLogo3.py
+# wrapper to check that all fasta files are same length
+
+"""
+import optparse, os, sys, subprocess, tempfile
+
+class WL3:
+    """
+    simple wrapper class to check fasta sequence lengths are all identical
+    """
+    FASTASTARTSYM = '>'
+    badseq = '## error - sequences in file %s are not all the same length - cannot proceed. Please read the tool documentation carefully'
+
+    def __init__(self,opts=None):
+        assert opts<>None,'WL3 class needs opts passed in - got None'
+        self.opts = opts
+        self.fastaf = file(self.opts.input,'r')
+        self.clparams = {}
+
+    def runCL(self):
+        """ construct and run a command line
+        """
+        cll = ['weblogo',]
+        cll += [' '.join(it) for it in list(self.clparams.items())]
+        cl = ' '.join(cll)
+        assert cl > '', 'runCL needs a command line as clparms'
+        fd,templog = tempfile.mkstemp(suffix='rgtempRun.txt')
+        tlf = open(templog,'w')
+        process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf)
+        rval = process.wait()
+        tlf.close()
+        tlogs = ''.join(open(templog,'r').readlines())
+        if len(tlogs) > 1:
+            s = '## executing %s returned status %d and log (stdout/stderr) records: \n%s\n' % (cl,rval,tlogs)
+        else:
+            s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl,rval)
+        os.unlink(templog) # always
+        return s
+
+        
+    def iter_fasta(self):
+        """
+        generator for fasta sequences from a file
+        """
+        aseq = []
+        seqname = None
+        for i,row in enumerate(self.fastaf):
+            if row.startswith(self.FASTASTARTSYM):
+                if seqname <> None: # already in a sequence
+                    s = ''.join(aseq)
+                    l = len(s)
+                    yield (seqname,l)
+                    seqname = row[1:].strip()
+                    aseq = []
+                else:
+                    if i > 0:
+                        print >> sys.stderr,'Invalid fasta file %s - does not start with %s' % (ffile,self.FASTASTARTSYM)
+                        sys.exit(1)
+                    else:
+                        seqname = row[1:].strip() 
+            else:
+                aseq.append(row.strip())
+        if seqname <> None: # last one
+            l = len(''.join(aseq))
+            yield (seqname,l)
+                
+        
+    def fcheck(self):
+        """ are all fasta sequence same length?
+        might be mongo big
+        """
+        flen = None
+        lasti = None
+        f = self.iter_fasta()
+        for i,(seqname,seqlen) in enumerate(f):
+	    lasti = i
+            if i == 0:
+                flen = seqlen
+            else:
+                if seqlen <> flen:
+                    print >> sys.stderr,self.badseq % self.opts.input
+                    sys.exit(1)
+        return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input,lasti,flen)
+
+
+    def run(self):
+        check = self.fcheck()
+        self.clparams['-f'] = self.opts.input
+        self.clparams['-o'] = self.opts.output
+        self.clparams['-t'] = '"%s"' % self.opts.logoname # must be wrapped as a string       
+        self.clparams['-F'] = self.opts.outformat       
+        if self.opts.size <> None:
+            self.clparams['-s'] = self.opts.size
+        if self.opts.lower <> None:
+            self.clparams['-l'] = self.opts.lower
+        if self.opts.upper <> None:
+            self.clparams['-u'] = self.opts.upper        
+        if self.opts.colours <> None:
+            self.clparams['-c'] = self.opts.colours
+        s = self.runCL()
+        return check,s
+
+
+if __name__ == '__main__':
+    '''
+    called as
+<command interpreter="python"> 
+    rgWebLogo3.py --outformat $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours"
+#if $range.mode == 'part'
+-l "$range.seqstart" -u "$range.seqend"
+#end if
+    </command>
+
+    '''
+    op = optparse.OptionParser()
+    op.add_option('-i', '--input', default=None)
+    op.add_option('-F', '--outformat', default='png')
+    op.add_option('-s', '--size', default=None) 
+    op.add_option('-o', '--output', default='rgWebLogo3')
+    op.add_option('-t', '--logoname', default='rgWebLogo3')
+    op.add_option('-c', '--colours', default=None)
+    op.add_option('-l', '--lower', default=None)
+    op.add_option('-u', '--upper', default=None)  
+    opts, args = op.parse_args()
+    assert opts.input <> None,'weblogo3 needs a -i parameter with a fasta input file - cannot open'
+    assert os.path.isfile(opts.input),'weblogo3 needs a valid fasta input file - cannot open %s' % opts.input
+    w = WL3(opts)
+    checks,s = w.run()
+    print >> sys.stdout, checks # for info

tools/rgenetics/rgWebLogo3.xml

@@ -1,7 +1,7 @@
-<tool id="weblogo3" name="Sequence Logo" version="0.1">
+<tool id="rgweblogo3" name="Sequence Logo" version="0.2">
    <description>generator for fasta (eg Clustal alignments)</description>
-   <command> 
-    weblogo -F $outformat -s $size -f $input -o $output -t "$logoname" -c "$colours"
+   <command interpreter="python"> 
+    rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours"
 #if $range.mode == 'part'
 -l "$range.seqstart" -u "$range.seqend"
 #end if