def main():
assert os.path.exists('in.fa')
assert os.path.exists('in.weights')
sanity_checks.sanity_check_fasta('in.fa')
num_size = int(os.popen("grep -c \">\" in.fa").read().strip())
if num_size <= cc_settings.MAX_SPLIT_IN_SIZE:
run_Cogent_on_input()
else:
dirs = split_files(input_filename='in.fa',
split_size=cc_settings.MAX_SPLIT_IN_SIZE)
run_Cogent_on_split_files(dirs, depth=0)
# align input to cogent2 gmap db so we can use it for evalution later;
run_gmap(dbname='cogent2', infile='in.trimmed.fa')
# clean up GMAP db files
if os.path.exists('cogent') and os.path.isdir('cogent'):
cleanup_gmap('cogent')
if os.path.exists('cogent2') and os.path.isdir('cogent2'):
cleanup_gmap('cogent2')
# rewrite cogent2.fa with prefix
f = open('cogent2.renamed.fasta', 'w')
for r in SeqIO.parse(open('cogent2.fa'), 'fasta'):
f.write(">{0}|{1}\n{2}\n".format(cc_settings.OUTPUT_PREFIX, r.id,
r.seq))
f.close()
def main():
assert os.path.exists('in.fa')
assert os.path.exists('in.weights')
sanity_checks.sanity_check_fasta('in.fa')
num_size = int(os.popen("grep -c \">\" in.fa").read().strip())
if num_size <= 20:
run_Cogent_on_input()
else:
dirs = split_files(input_filename='in.fa', split_size=20)
run_Cogent_on_split_files(dirs)
def main():
assert os.path.exists("in.fa")
assert os.path.exists("in.weights")
sanity_checks.sanity_check_fasta("in.fa")
num_size = int(os.popen('grep -c ">" in.fa').read().strip())
if num_size <= 20:
run_Cogent_on_input()
else:
dirs = split_files(input_filename="in.fa", split_size=20)
run_Cogent_on_split_files(dirs)
def main():
assert os.path.exists('in.fa')
assert os.path.exists('in.weights')
sanity_checks.sanity_check_fasta('in.fa')
num_size = int(os.popen("grep -c \">\" in.fa").read().strip())
if num_size <= cc_settings.MAX_SPLIT_IN_SIZE:
run_Cogent_on_input()
else:
dirs = split_files(input_filename='in.fa', split_size=cc_settings.MAX_SPLIT_IN_SIZE)
run_Cogent_on_split_files(dirs, depth=0)
# clean up GMAP db files
if os.path.exists('cogent') and os.path.isdir('cogent'):
cleanup_gmap('cogent')
if os.path.exists('cogent2') and os.path.isdir('cogent2'):
cleanup_gmap('cogent2')