From 635a90bd2eebdd9b9ff56086ffcf7ffd41239d7a Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 19 May 2011 08:43:33 +0000
Subject: [PATCH] initial checkin
SVN: 21384
---
.../source/Python/solexaQa.py | 54 +++++++++++++++++++
1 file changed, 54 insertions(+)
create mode 100644 deep_sequencing_unit/source/Python/solexaQa.py
diff --git a/deep_sequencing_unit/source/Python/solexaQa.py b/deep_sequencing_unit/source/Python/solexaQa.py
new file mode 100644
index 00000000000..e95dd73616e
--- /dev/null
+++ b/deep_sequencing_unit/source/Python/solexaQa.py
@@ -0,0 +1,54 @@
+#!/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...")
--
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