Commit 2c1fc3c7 by Robin Erich Muench

fixed python3 TypeError, tab/spaces inconsistency, git link

parent 49fec2dc
......@@ -9,7 +9,7 @@ Download
Via Git:
git clone git@git.embl.de:costea/metaSNV.git
git clone https://git.embl.de/costea/metaSNV.git
or [download](https://git.embl.de/costea/metaSNV/repository/archive.zip?ref=master) a zip file of the repository.
......
......@@ -76,16 +76,16 @@ def compute_opt(args):
def get_header(args):
use = open(args.all_samples).readline().rstrip()
o = subprocess.check_output(["samtools","view","-H",use])
o = subprocess.check_output(["samtools","view","-H",use]).decode("utf-8")
f = open(args.project_dir + '/bed_header','w')
for line in o.split('\n')[1:]:
line = line.rstrip().split('\t')
if len(line) != 3:
continue
line[1] = line[1].replace('SN:','')
line[2] = line[2].replace('LN:','')
f.write(line[1]+'\t1\t'+line[2]+'\n')
f.close()
line = line.rstrip().split('\t')
if len(line) != 3:
continue
line[1] = line[1].replace('SN:','')
line[2] = line[2].replace('LN:','')
f.write(line[1]+'\t1\t'+line[2]+'\n')
f.close()
args.ctg_len = args.project_dir + '/bed_header'
def compute_summary(args):
......@@ -96,14 +96,14 @@ def compute_summary(args):
cov_files = glob(cov_dir + '/*.cov')
if not cov_files:
if not args.print_commands:
stderr.write("Coverage files not found.\n")
else:
stderr.write("Coverage files not found.\nFinish running the commands printed above and then run this command again.\n")
if not args.print_commands:
stderr.write("Coverage files not found.\n")
else:
stderr.write("Coverage files not found.\nFinish running the commands printed above and then run this command again.\n")
exit(1)
for f in cov_files:
cmd = ['python',
path.join(basedir, 'src/computeGenomeCoverage.py'),
path.join(basedir, 'src/computeGenomeCoverage.py'),
f,
f + '.detail',
f + '.summary']
......@@ -115,7 +115,7 @@ def compute_summary(args):
cmd = ['python',
'{}/src/collapse_coverages.py'.format(basedir),
args.project_dir]
subprocess.call(cmd)
subprocess.call(cmd)
def split_opt(args):
......@@ -129,7 +129,7 @@ def split_opt(args):
for f in older_files:
os.unlink(f)
project_name = path.basename(args.project_dir)
project_name = path.basename(args.project_dir)
print("\nCalculating best database split:")
# usage createOptimumSplit.sh <all_cov.tab> <all_perc.tab> <geneDefinitions> <INT_NrSplits> <.outfile>
......@@ -246,26 +246,26 @@ SOLUTION: run getRefDB.sh or set up a custom database before running metaSNP cal
exit(1)
if not path.isfile(basedir+"/src/qaTools/qaCompute") or not path.isfile(basedir+"/src/snpCaller/snpCall"):
stderr.write('''
stderr.write('''
ERROR: No binaries found
SOLUTION: make\n\n'''.format(basedir))
exit(1)
SOLUTION: make\n\n'''.format(basedir))
exit(1)
if args.threads > 1 and args.n_splits==1:
args.n_splits=args.threads
args.n_splits=args.threads
if path.exists(args.project_dir) and not args.print_commands:
stderr.write("Project directory '{}' already exists\n\n\n".format(args.project_dir))
stderr.write("Project directory '{}' already exists\n\n\n".format(args.project_dir))
exit(1)
create_directories(args.project_dir)
compute_opt(args)
compute_summary(args)
get_header(args)
if args.n_splits > 1:
split_opt(args)
split_opt(args)
snp_call(args)
if __name__ == '__main__':
......
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