Commit cf423e71 authored by Robin Erich Muench's avatar Robin Erich Muench
Browse files

Merge branch 'master' into 'master'

DOC Spell check comments

See merge request !6
parents 70ce9fa7 07b1c519
......@@ -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']
......
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')
......
......@@ -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))
......
......@@ -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
......
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