Update paths for results scripts

parent 4b011eed
......@@ -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__':
......
......@@ -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
......
......@@ -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()
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment