[med-svn] [qcumber] 01/03: Imported Upstream version 1.0.1+dfsg

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository qcumber.

commit 52fe08c5dcb9eb9af495c98a6f83fba64d12045f
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 29 16:34:00 2016 +0100

    Imported Upstream version 1.0.1+dfsg
---
 QCumber.py | 51 +++++++++++++++++++++++++++------------------------
 1 file changed, 27 insertions(+), 24 deletions(-)

diff --git a/QCumber.py b/QCumber.py
index c21b0eb..303edfe 100755
--- a/QCumber.py
+++ b/QCumber.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 __author__ = 'LieuV'
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 from classes import *
 from helper import *
@@ -305,23 +305,21 @@ def main(arguments):
 			# Case 1: Folder contains fastq files
 			if len([x for x in input if isfile(x) and any([x.endswith(ext) for ext in file_extensions]) ])>0:
 				input= [x for x in input if isfile(x) and any([x.endswith(ext) for ext in file_extensions]) ]
-				if arguments["technology"].startswith("Illumina"):
-					for setname, files in groupby(input, key=lambda x: "_".join(x.split("_")[:-3])):
-						#for setname, files in groupby(files, key=lambda x: "_".join(x.split("_")[:-2])):
-						temp_file =  sorted(list(files))
-						r1_reads = [x for x in  temp_file if r1_pattern in x]
-						r2_reads = [x for x in temp_file if r2_pattern in x]
-						myFiles.append([r1_reads, r2_reads])
-				else:
-					# IonTorrent
-					#for setname, files in groupby(input, key=lambda x: "_".join(x.split("_")[:-2])):
-					#	temp_file = sorted(list(files))
-					# TODO Changed
-					myFiles = input
-					#r1_reads = [x for x in input if r1_pattern in x]
-					#r2_reads = [x for x in input if r2_pattern in x]
-					#myFiles.append([r1_reads, r2_reads])
-
+				if len(input)!=0:
+					if arguments["technology"].startswith("Illumina"):
+						for setname, files in groupby(input, key=lambda x: "_".join(x.split("_")[:-3])):
+							#for setname, files in groupby(files, key=lambda x: "_".join(x.split("_")[:-2])):
+							temp_file =  sorted(list(files))
+							r1_reads = [x for x in  temp_file if r1_pattern in x]
+							r2_reads = [x for x in temp_file if r2_pattern in x]
+							if len(r1_reads) != 0:
+								if len(r2_reads) != 0:
+									myFiles.append([r1_reads, r2_reads])
+								else:
+									myFiles.append(r1_reads)
+					else:
+						# IonTorrent
+						myFiles = input
 			# Case 2: Folder contains subfolder for each sample
 			else:
 				input = [x for x in input if os.path.isdir(x)]
@@ -334,7 +332,11 @@ def main(arguments):
 								temp_file = sorted(list(files))
 								r1_reads = [x for x in temp_file if r1_pattern in x]
 								r2_reads = [x for x in temp_file if r2_pattern in x]
-								myFiles.append([r1_reads, r2_reads])
+								if len(r1_reads)!=0:
+									if len(r2_reads)!=0:
+										myFiles.append([r1_reads, r2_reads])
+									else:
+										myFiles.append(r1_reads)
 						else:
 							myFiles.append(sorted(list(files)))
 					files = None
@@ -351,6 +353,7 @@ def main(arguments):
 				myFiles.append([arguments["r1"]])
 
 		print("Found " + str(len(myFiles)) + " sample(s).")
+
 		for subset in myFiles:
 			print("Analyse " + str(i) + "/" + str(len(myFiles)))
 
@@ -488,7 +491,7 @@ if __name__ == "__main__":
 	parser.add_argument('-threads', dest='threads', default = 4, type = int)
 	parser.add_argument('-adapter', dest = 'adapter', choices = ['TruSeq2-PE', 'TruSeq2-SE' , 'TruSeq3-PE' , 'TruSeq3-SE' , 'TruSeq3-PE-2', 'NexteraPE-PE' ])
 	parser.add_argument('-reference', dest='reference', required = False, help = "Map reads against reference")
-	parser.add_argument('-index', dest='index', required = False, help = "Mapping index")
+	parser.add_argument('-index', dest='index', required = False, help = "Bowtie2 index if available.")
 	parser.add_argument('-sav', dest='sav', required=False,help="Illumina folder for SAV. Requires RunInfo.xml, RunParamter.xml and Interop folder.")
 
 	parser.add_argument('-save_mapping', action = "store_true")
@@ -499,10 +502,10 @@ if __name__ == "__main__":
 	parser.add_argument('-version', action='version', version='%(prog)s v' + __version__)
 	parser.add_argument('-nokraken', action = "store_true")
 	parser.add_argument('-nomapping', action = "store_true")
-	parser.add_argument('-trimBetter', action = "store_true")
-	parser.add_argument('-trimBetter_threshold', dest='trimBetter_threshold', help = "Default setting for Illumina: 0.15 and for IonTorrent: 0.25.", required=False, type=float)
-	parser.add_argument('-forAssembly', action = "store_true", help = "Trim parameter are optimized for assemblies (trim more aggressive).")
-	parser.add_argument('-forMapping', action = "store_true", help = "Trim parameter are optimized for mapping (allow more errors).")
+	parser.add_argument('-trimBetter', action = "store_true", help= "Optimize trimming parameter using 'Per sequence base content' from fastqc. Not recommended for amplicons.")
+	parser.add_argument('-trimBetter_threshold', dest='trimBetter_threshold', help = "Set -trimBetter to use this option.Default setting for Illumina: 0.15 and for IonTorrent: 0.25.", required=False, type=float)
+	parser.add_argument('-forAssembly', action = "store_true", help = "Set -trimBetter to use this option.Trim parameter are optimized for assemblies (trim more aggressive).")
+	parser.add_argument('-forMapping', action = "store_true", help = "Set -trimBetter to use this option.Trim parameter are optimized for mapping (allow more errors).")
 
 	arguments = vars(parser.parse_args())
 	main(arguments)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/qcumber.git