initial checkin

SVN: 21384

deep_sequencing_unit/source/Python/solexaQa.py

+#!/usr/bin/env python
+'''
+Python Wrapper for a perl based program.
+Generates tile based quality graphics
+
+Output: pdf 
+@author: Manuel Kohler
+@copyright: ETH Zurich
+@precondition: Working pdftk and SolexaQA.pl binaries
+
+'''
+
+import subprocess
+import shlex
+import os
+import sys
+from optparse import OptionParser
+
+SCRIPT = "/usr/local/dsu/bin/SolexaQA/SolexaQA.pl"
+PDFTK = '/usr/local/dsu/pdftk-1.41/pdftk/pdftk'
+
+parser = OptionParser()
+parser.add_option("-p", "--path", dest="path", action="store", type="string",
+                  help="Path of the fastq files", metavar="PATH")
+parser.add_option("-v", dest="verbose", action="store_true",
+                  help="tell me all")
+(options, args) = parser.parse_args()
+path = options.path
+os.chdir(path)
+
+listdir = os.listdir(path)
+for file in listdir:
+  if file.endswith('fastq'):
+    args = SCRIPT + " -sanger " + path + "/" + file
+    Newargs = shlex.split(args)
+    p = subprocess.Popen(Newargs)
+    p.wait()
+    #convert -page A4 ETHZ_BSSE_110204_62Y8YAAXX_7.fastq.png  ETHZ_BSSE_110204_62Y8YAAXX_7.fastq_TileStatistics_A4.pdf
+    convert = ['convert', '-page', 'A4', file + '.png', file + '.png.pdf']
+    c = subprocess.Popen(convert)
+    c.wait()
+    #rm *.matrix *.segments *.quality *.png
+    os.remove(file + '.matrix')
+    os.remove(file + '.segments')
+    os.remove(file + '.quality')
+    os.remove(file + '.png')
+   
+    files = file + '.segments.hist.pdf', file + '.quality.pdf', file + '.png.pdf' 
+    assemble = [ PDFTK, 'cat', 'output', file.replace('.', '_', 1) + '_SolexaQA.pdf']
+    [assemble.insert(1, i) for i in files]
+    a = subprocess.Popen(assemble)
+    a.wait()
+    [os.remove(f) for f in files] 
+print("Finished...")