def mapFastqFiles(genome):
if "main" in inspect.stack()[1][3]:
dir = INPUT_DIR
else:
dir = OUTPUT_DIR
filename_1 = dir + genome + ".fastq"
filename_2 = dir + genome + "_1.fastq"
filename_3 = dir + genome + "_2.fastq"
se_exists = False
if os.path.isfile(filename_1):
print "Single End mapping"
command1 = (
"bwa mem -t#cpus ref_files/TB_H37Rv_sequence_validated.fa "
+ filename_1
+ " > "
+ OUTPUT_DIR
+ genome
+ "_se.sam"
)
os.system(command1)
se_exists = True
command2 = (
"bwa mem -t#cpus ref_files/TB_H37Rv_sequence_validated.fa "
+ filename_2
+ " "
+ filename_3
+ " > "
+ OUTPUT_DIR
+ genome
+ "_pe.sam"
)
os.system(command2)
if se_exists:
"Merging sams"
command3 = (
"run_picard MergeSamFiles INPUT="
+ OUTPUT_DIR
+ genome
+ "_se.sam"
+ " INPUT="
+ OUTPUT_DIR
+ genome
+ "_pe.sam"
+ " OUTPUT="
+ OUTPUT_DIR
+ genome
+ ".sam"
)
else:
command3 = "mv " + OUTPUT_DIR + genome + "_pe.sam " + OUTPUT_DIR + genome + ".sam"
os.system(command3)
if se_exists:
command4 = "rm -rf " + OUTPUT_DIR + genome + "_se.sam"
command5 = "rm -rf " + OUTPUT_DIR + genome + "_pe.sam"
os.system(command4)
os.system(command5)
processSamFiles(genome)
def main():
if len(sys.argv) < 2:
sys.stderr.write('USAGE: python processGenomes.py <Genome List>\n')
sys.exit(1)
in_file = sys.argv[1]
genome_list = {}
files = os.listdir(INPUT_DIR)
with open(in_file, 'r') as infile:
for line in infile.readlines():
genome = line.strip()
exists = False
for name in files:
if genome in name and not exists:
ext = name.split('.')[1].strip()
if ext in EXT_DICT.keys():
genome_list[genome] = EXT_DICT[ext]
exists = True
if not exists:
sys.stderr.write('No corresponding input file found for genome ' + genome + '!\n')
count = 0
outfile = open('Mutation-analysis.log', 'w')
for genome in genome_list.keys():
step = genome_list[genome]
if step == 1:
mapFastqFiles(genome)
elif step == 2:
processSamFiles(genome)
elif step == 3:
processBamFiles(genome)
elif step == 4:
getAnnotations(genome)
count = count + 1
if count % 100 == 0:
write_data = 'Processed ' + str(count) + ' genomes ...'
print write_data
outfile.write(write_data + '\n')
outfile.close()
