Ignore empty lines in sample.list

README.md

@@ -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`

getResults.py

@@ -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)

str_outliers.py

@@ -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)