Update paths for results scripts

getResults.py

@@ -122,9 +122,9 @@ def get_results(locus, region, samples):
             if sample not in previous_results:
                 file_path = os.path.join(input_directory, sample)
                 print(file_path)
-                eh = get_eh_results(os.path.join(file_path, f'eh/{sample}.vcf'), region)
-                tred = get_tred_results(os.path.join(file_path, f'tredparse/{sample}.tred.vcf.gz'), region)
-                gang = get_gang_results(os.path.join(file_path, f'gangstr/{sample}.vcf'), region)
+                eh = get_eh_results(os.path.join(file_path, f'str/eh/{sample}.vcf'), region)
+                tred = get_tred_results(os.path.join(file_path, f'str/tredparse/{sample}.tred.vcf.gz'), region)
+                gang = get_gang_results(os.path.join(file_path, f'str/gangstr/{sample}.vcf'), region)
                 result_file.write(f'{sample}\t{eh}\t{tred}\t{gang}\n')
 
 if __name__ == '__main__':

launch_str_outliers.sh

@@ -21,7 +21,7 @@ then
 fi
 
 SCRIPT="$(dirname "$(readlink -f "$0")")/str_outliers.py"
-SAMPLES="$(dirname "$(readlink -f "$0")")/$SAMPLES"
+SAMPLES="$(readlink -f "$SAMPLES")"
 
 cd "$RESULTS_OUTPUTDIR" || exit 1
 

str_outliers.py

@@ -6,7 +6,6 @@
 ## Author : Anne-Sophie Denommé-Pichon
 ## Description : script to get automatically outliers from expansion pipeline results from getResults.py
 
-
 import collections
 import csv
 import logging
@@ -16,8 +15,6 @@ import os.path
 import scipy.stats
 import sys
 
-
-
 output_directory = None
 zscore_threshold = None
 percentile_threshold = None
@@ -163,7 +160,7 @@ def display_outliers(locus, limits, samples):
 
 if __name__ == '__main__':
     if len(sys.argv) != 3:
-        print(f'Usage: {sys.argv[0].split(os.sep)[-1]} <LOCUS> <SAMPLE.LIST>', file=sys.stderr)
+        print(f'Usage: {sys.argv[0].split(os.sep)[-1]} <LOCUS> <SAMPLES.LIST>', file=sys.stderr)
         sys.exit(1)
     with open(sys.argv[2]) as samples_list:
         samples = set()