initial checkin

SVN: 21383

deep_sequencing_unit/source/Python/concatenatePdfs.py

+#!/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__()