Modified generate_weblogo. Added weblogo 3 support

Author: rfarouni

haystack/external.py

@@ -1207,19 +1207,24 @@ def pwm_from_meme_file(meme_filename,motif_id):
             return pwm   
 
 
-def generate_weblogo(motif_id,meme_filename,output_filename,file_format='PNG',title=None,scale=2.0):
+def generate_weblogo(motif_id,meme_filename,output_filename,file_format='png',title=None):
+
+    if title==None: title = output_filename
+
+    output_filename = output_filename + '.' + file_format
 
     pwm=pwm_from_meme_file(meme_filename,motif_id)
     meme_motif=Motif_from_counts(pwm)
 
     kmers   = meme_motif.bogus_kmers(100)
-    width   = float(len(kmers[0]) ) *scale
+    #width   = float(len(kmers[0]) ) *scale
     #height  = float(4)
     #width, height = width*scale, height*scale
     tmp     = tempfile.mktemp() + '.fsa'
-    if title==None: title = output_filename
     seqs2fasta(kmers,tmp)
-    cmd = 'weblogo -F %s  --errorbars NO  --fineprint ""  --upper %d  -A dna  -f %s  -o %s  -t "%s" '%(file_format,width, tmp, output_filename, title)
+
+    tmp= "/home/rick/cap.fa"
+    cmd = 'weblogo -F %s  -A dna  -f %s  -o %s  -t "%s"   --errorbars NO  --fineprint "" '%(file_format, tmp, output_filename, title)
     #print cmd 
     sb.call(cmd,shell=True)