Analyse dubletter Barcodes

barcode-analyse.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+# Ermitteln von Dubletten in Barcodes
+
+mkdir -p output output/barcodes
+
+# Bibliotheca Barcodes extrahieren
+for f in input/*.imp; do
+  grep '^\*I BARCO ' "$f" | dos2unix | cut -c 10- > output/barcodes/"${f##*/}.txt"
+done
+# Alephino Barcodes extrahieren
+for f in input/*-exemplare.txt; do
+  grep '^120 ' "$f" | cut -c 6- > output/barcodes/"${f##*/}.txt"
+done
+
+# Dubletten ermitteln
+sort output/barcodes/*.txt | uniq -d > output/barcodes/duplicates
+(cd output/barcodes && for f in *.txt ; do
+  grep -FxH -f duplicates "$f" | sort | join -o 2.1 -t ':' -a1 -2 2 duplicates - | cut -d '.' -f 1 > "${f}".tmp
+done)
+paste output/barcodes/duplicates output/barcodes/*.tmp | awk -F $'\t' '{sub($1, "\"&\""); print}' > output/barcodes/duplicates.tsv && rm output/barcodes/*.tmp