Add script to get STR tools results at the fragile X locus

getFMR1result.sh

+#! /bin/sh
+
+### ASDP PIPELINE ###
+## pipeline.sh
+## Version : 0.0.1
+## Licence : FIXME
+## Description : script to get automatically results from pipeline.sh script in a tsv format on the FMR1 X fragile locus
+## Usage : 
+## Output : FIXME
+## Requirements : FIXME
+
+## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Creation Date : 20191215
+## last revision date : 20191215
+## Known bugs : None
+
+cd /work/gad/shared/analyse/STR/pipeline/
+(
+    echo -e 'dijenxxx\tEH\tTred\tGangSTR'
+    ls -d dijen* | while read dijen
+    do
+        (
+            echo "$dijen"
+            awk '$1 == "chrX" && $2 == "146993568" {print $5}' $dijen/eh/$dijen.vcf |
+                sed 's@<STR\([0-9]\+\)>@\1@g'
+            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}'
+            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(".")'
+        ) |
+            tr '\n' '\t'
+        echo
+    done
+) > results
+
+