Ignore empty lines in sample.list

parent fcbfaac5
......@@ -6,7 +6,7 @@
- Licence: AGPLv3
- Description: How to launch scripts to get STR genotype from genomes on all the locus tested
1. Create `samples.list`
1. Create `samples.list` (bam file names without .bam)
2. Fill the configuration file `config.sh`.
3. Launch `launch_pipeline.sh`: `nohup ./launch_pipeline.sh samples.list &`. Dependencies :
- `config.sh`
......
......@@ -133,8 +133,10 @@ if __name__ == '__main__':
sys.exit(1)
with open(sys.argv[1]) as samples_list:
samples = []
for sample in sorted(samples_list.readlines()):
samples.append(sample.rstrip())
for line in sorted(samples_list.readlines()):
sample = line.rstrip()
if sample:
samples.append(sample)
os.makedirs(output_directory, exist_ok=True)
for locus, region in enumerate_variants(variant_catalog):
print(locus, region)
......
......@@ -167,7 +167,9 @@ if __name__ == '__main__':
sys.exit(1)
with open(sys.argv[2]) as samples_list:
samples = set()
for sample in samples_list.readlines():
samples.add(sample.rstrip())
for line in samples_list.readlines():
sample = line.rstrip()
if sample:
samples.add(sample)
limits = load_limits()
display_outliers(sys.argv[1], limits, samples)
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