Merge branch 'master' into 'master'

DOC Spell check comments

See merge request !6

metaSNP_filtering.py

@@ -25,7 +25,7 @@ def get_arguments():
 	parser.add_argument("--debug", action="store_true", help=argparse.SUPPRESS)
 	parser.add_argument("-v", "--vcf", action="store_true", help=argparse.SUPPRESS)#"output variants in variant call format (vcf4.2)"
 	
-#	TODO: POPULAITON STATISTICS
+#	TODO: POPULATION STATISTICS
 	## Population Statistics (Fst - ):
 #	parser.add_argument("-f", "--fst", action="store_true")
 	## pNpS ratio:
@@ -51,7 +51,7 @@ def get_arguments():
 	##############################
 
 def debugging(taxids_of_interest, header_cov):
-	'''SanityCheck for the Dict of TaxID:Samples'''
+	'''Sanity check for the Dict of TaxID:Samples'''
 	
 	nr_keys = 0
 	taxids_of_interest = []
@@ -252,10 +252,10 @@ def header_comparison(header_cov):
 
 	
 #################################
-## FILTER II: ACQUIRE SNPs WITH SUFFICIENT OCCURENCE WITHIN SAMPLES_OF_INTERES
+## FILTER II: ACQUIRE SNPs WITH SUFFICIENT OCCURRENCE WITHIN SAMPLES_OF_INTEREST
 #  --SNP Conditions (Default):
 #           1. Position covered by at least (5) reads
-#           2. Position present in at least 50 % of the accepted samples_of_interes
+#           2. Position present in at least 50 % of the accepted samples_of_interest
 
 def filter_two(args, snp_header):
 	'''position wise filtering'''
@@ -440,9 +440,9 @@ if __name__ == "__main__":
 	if args.debug:
 		print_arguments()
 
-#=========================================
-# Filtering I - Determine Taxa of Interes:
-#=========================================
+#==========================================
+# Filtering I - Determine Taxa of Interest:
+#==========================================
 
 	samples_of_interest = relevant_taxa(args)['SoI']
 	header_cov = relevant_taxa(args)['h']

src/computeGenomeCoverage.py

 import sys
 
-#We assume that contings are sorted within the genome, so that a contig won't show up 
-#randomly in the file, but together with its friends.
+# We assume that contigs are sorted within the genome
 
 cov = open(sys.argv[1],'r')
 xcov = open(sys.argv[2],'r')

src/createOptimumSplit.py

@@ -55,7 +55,9 @@ print 'Found %d genomes again. Hope they match'%(len(percDict))
 
 
 table = []
-#Get an approximation of how many reads hit each genome. This is as close as you will get to figuring out how long running it is going to take
+# Get an approximation of how many reads hit each genome. This is as close as
+# you will get to figuring out how long running it is going to take
+
 for k in genomeDict.keys():
     read = genomeDict[k]*covDict[k]/100 #*percDict[k]/100
     table.append((k,read))

src/snpCaller/call_vC.cpp

@@ -131,7 +131,7 @@ bool indexGenomeAndGenes(FILE* refGenome, FILE* refGenes) {
     const char* l = toksplit(line,'\t',tok,10000);
     int pos = 0;
     while (*l) {
-      if (pos == 2) {//Thie is the name!                                                                      
+      if (pos == 2) {//This is the name!                                                                      
 	if (name.compare("") == 0) {//This is the first one
 	  name = tok;
 	} else if (name.compare(tok) != 0) {//Boom, this is a new one