Lesser changes to text outputs

consam.py

@@ -27,7 +27,7 @@
 import pickle
 import argparse
 
-parser = argparse.ArgumentParser(description='Convert any stream of reads to a pickle file for WISECONDOR, defaults are set for the SAM format.',
+parser = argparse.ArgumentParser(description='Convert any stream of reads to a pickle file for WISECONDOR, defaults are set for the SAM format',
 		formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
 parser.add_argument('outfile', type=str,

countgc.py

@@ -27,7 +27,7 @@
 import pickle
 import argparse
 
-parser = argparse.ArgumentParser(description='Create GC-count file for GC-corrections. Outputs table as pickle to a specified output file.',
+parser = argparse.ArgumentParser(description='Create GC-count file for GC-corrections. Outputs table as pickle to a specified output file',
 		formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
 parser.add_argument('reffile', type=str,

newref.py

@@ -29,7 +29,7 @@
 import gcc
 import argparse
 
-parser = argparse.ArgumentParser(description='Create a new reference table from a set of reference samples. Outputs table as pickle to a specified output file.',
+parser = argparse.ArgumentParser(description='Create a new reference table from a set of reference samples, outputs table as pickle to a specified output file',
 		formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
 parser.add_argument('refdir', type=str,

plot.py

@@ -137,15 +137,13 @@ def preparePlot(chrom):
 
 if __name__ == "__main__":
 	import argparse
-	parser = argparse.ArgumentParser(description='WISECONDOR \
-		(WIthin-SamplE COpy Number aberration DetectOR): \
-		Detect fetal trisomies and smaller CNV\'s in a maternal plasma sample.',
+	parser = argparse.ArgumentParser(description='Plot results generated by WISECONDOR',
 		formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
 	parser.add_argument('plotdata', type=str,
 					   help='datafile as output by test.py')
 	parser.add_argument('outfile', type=str,
-					   help='output file to store plot in')
+					   help='output file to store plot in, .pdf is added as extension')
 
 	parser.add_argument('-mpluse', default='agg', type=str, 
 					help='make matplotlib use another backend for plotting')

test.py

@@ -270,7 +270,7 @@ def testTrisomyStoufferDirect(zScoresDict):
 import argparse
 parser = argparse.ArgumentParser(description='WISECONDOR \
 	(WIthin-SamplE COpy Number aberration DetectOR): \
-	Detect fetal trisomies and smaller CNV\'s in a maternal plasma sample.',
+	Detect fetal trisomies and smaller CNV\'s in a maternal plasma sample',
 	formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
 parser.add_argument('sample', type=str,
@@ -359,6 +359,7 @@ def testTrisomyStoufferDirect(zScoresDict):
 print '\nChromosome wide, aneuploidy test:'
 testTrisomyStoufferDirect(zScoresDict)
 
+print '\n\n# Script information:\n'
 print '\nComputing additional data for plots'
 wastedBins = dict()
 for chrom in range(1,23):
@@ -380,9 +381,3 @@ def testTrisomyStoufferDirect(zScoresDict):
 pickle.dump(outputData,open(args.outfile,'wb'))
 
 print '\n# Finished'
-
-quit()
-
-print '\n\n# Script information:\n'
-plotResults(sample,markedBins,kept,kept2,outputBase,zScoresDict,zSmoothDict,blindsDict)
-