Add script to get STR tools results at all locus

getResults.py

+#! /usr/bin/env python3
+
+### ASDP PIPELINE ###
+## getResults.py
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to get automatically results from pipeline.sh script in a tsv format on all the locus
+## Usage : 
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20191215
+## last revision date : 20191215
+## Known bugs : None
+
+import glob
+import json
+import logging
+import os
+import os.path
+import re
+
+variants_catalog = '/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json'
+input_directory ='/work/gad/shared/analyse/STR/pipeline/'
+output_directory ='/work/gad/shared/analyse/STR/results/'
+
+def enumerate_variants(catalog_path):
+    with open(catalog_path) as catalog_file:
+        variants = json.load(catalog_file)
+
+        for variant in variants:
+            region = variant['ReferenceRegion']
+            # TODO handle other regions?
+            if isinstance(region, list):
+                region = region[0]
+            chrom, pos = region.split(':')
+            pos = pos.split('-')[0]
+            yield variant['LocusId'], (chrom, pos)
+
+def get_eh_results(file_path, region):
+    try:
+        with open(file_path) as eh_file:
+            for line in eh_file:
+                columns = re.split(r'[ \t]+', line)
+                # TODO FIXME allow for some difference in position
+                if len(columns) >= 2 and columns[0] == region[0] and columns[1] == region[1]:
+                    return re.sub('<STR([0-9]+)>', '\g<1>', columns[4])
+        return '.'
+    except FileNotFoundError:
+        logging.warn(f'File not found "{file_path}"')
+        return 'nofile'
+
+def get_tred_results(file_path, region):
+#             gunzip -c $dijen/tredparse/$dijen.tred.vcf.gz |
+#                 awk '$1 == "chrX" && $2 == "146993569" && $3 == "FXS" {print $8}' |
+#                 tr ';' '\n' |
+#                 awk -F '=' '$1 == "RPA" {print $2}'
+    return 'FIXME'
+
+def get_gang_results(file_path, region):
+#             awk '$1 == "chrX" && $2 == "146993569" {print $9 " " $10}' $dijen/gangstr/$dijen.vcf |
+#                 python3 -c 'import sys; format, genotype = sys.stdin.read().split(); print(genotype.split(":")[format.split(":").index("REPCN")]) if genotype != "." else print(".")'
+    return 'FIXME'
+
+def get_results(locus, region):
+    with open(os.path.join(output_directory, locus + '.tsv'), 'w') as result_file:
+        result_file.write('dijenxxx\tEH\tTred\tGangSTR\n')
+        for file_path in sorted(glob.glob(os.path.join(input_directory, 'dijen*'))):
+            file_name = file_path.split(os.sep)[-1]
+            eh = get_eh_results(os.path.join(file_path, f'eh/{file_name}.vcf'), region)
+            tred = get_tred_results(os.path.join(file_path, f'tredparse/{file_name}.vcf.gz'), region)
+            gang = get_gang_results(os.path.join(file_path, f'gangstr/{file_name}.vcf'), region)
+            result_file.write(f'{file_name}\t{eh}\t{tred}\t{gang}\n')
+
+if __name__ == '__main__':
+    os.makedirs(output_directory, exist_ok=True)
+    for locus, region in enumerate_variants(variants_catalog):
+        get_results(locus, region)
+        break # TODO remove
+