From 1db4d16f39a87f419cbaa58813b5f1022d45b2ee Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 19 May 2011 08:43:20 +0000
Subject: [PATCH] initial checkin
SVN: 21383
---
.../source/Python/concatenatePdfs.py | 70 +++++++++++++++++++
1 file changed, 70 insertions(+)
create mode 100644 deep_sequencing_unit/source/Python/concatenatePdfs.py
diff --git a/deep_sequencing_unit/source/Python/concatenatePdfs.py b/deep_sequencing_unit/source/Python/concatenatePdfs.py
new file mode 100644
index 00000000000..715ca5e670e
--- /dev/null
+++ b/deep_sequencing_unit/source/Python/concatenatePdfs.py
@@ -0,0 +1,70 @@
+#!/usr/bin/python
+'''
+Concatenates several pdfs in a given directory depending
+on the lane number in the file name.
+This number is defined as the last number in the file name
+separated by '_'
+The concatenated file will be named:
+flow_cell + '_' + lane + '_quality.pdf'
+
+@author: Manuel Kohler
+@copyright: ETH Zurich
+@precondition: Working pdftk installation
+'''
+
+import os
+import fnmatch
+import subprocess
+from optparse import OptionParser
+
+PDFTK = '/usr/local/dsu/pdftk-1.41/pdftk/pdftk'
+LANES = 8
+
+class pdfList(list):
+ def __init__ (self, lane, pdfs=[]):
+ list.__init__([])
+ self.lane = lane
+ self.extend(pdfs)
+
+def options():
+ parser = OptionParser()
+ parser.add_option("-p", "--path", dest="path", action="store", type="string",
+ help="Path of the fastq files", metavar="PATH")
+ (options, args) = parser.parse_args()
+ return (options.path)
+
+def concatenatePdfs(file_list, lane):
+ # take the first list element as a reference for the final pdf name
+ flow_cell = '_'.join(file_list[0].split('_', 4)[0:4])
+ print(flow_cell)
+ new_name = flow_cell + '_' + lane + '_quality.pdf'
+ args = [PDFTK, 'cat', 'output', new_name]
+ [args.insert(1, i) for i in file_list]
+ a = subprocess.Popen(args)
+ a.wait()
+ [os.remove(file) for file in file_list]
+
+def createPdfList (lane):
+ path = options()
+ # create pdf list depending on lane
+ ll = 'lane' + lane
+ vars()[ll] = pdfList(lane)
+
+ for file in os.listdir(path):
+ if fnmatch.fnmatch(file, '*.pdf'):
+ for l in (file.split('_')[4]):
+ if (l == lane):
+ (vars()[ll]).append(file)
+ vars()[ll].sort()
+ return (vars()[ll])
+
+def __main__():
+ list_of_pdfs = []
+ for i in range(1, LANES + 1):
+ l = createPdfList(str(i))
+ list_of_pdfs.append(l)
+
+ [concatenatePdfs(list_of_pdfs[i], list_of_pdfs[i].lane) for i in range(len(list_of_pdfs))]
+ print("DONE...")
+
+__main__()
--
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