--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/db_resfinder/CHECK-entries.sh	Mon Jan 10 20:06:07 2022 +0000
@@ -0,0 +1,63 @@
+#!/bin/sh
+#
+# CHECK-entries.sh
+# Marco van Zwetselaar <zwets@kcri.ac.tz>
+#
+#  Checks that each sequence in the fsa files has an entry in phenotypes.txt,
+#  and that every entry in phenotypes has a corresponding sequence in an fsa.
+#
+#  Writes to stdout the lists of missing entries, as well as close matches
+#  based on allele ID or accession.
+#
+
+# Echo all identifiers from the phenotypes.txt file, one per line.
+phenotype_ids() {
+    cut -f1 phenotypes.txt | tail -n +2 | sed -e 's/ *$//'
+}
+
+# Echo all sequence identifiers from the *.fsa, one per line.
+sequence_ids() {
+    fgrep -h '>' *.fsa | sed -e 's/>\([^ ]*\).*/\1/'
+}
+
+# Filter stdin for near matches of seqid $1.  A near match is when either
+# the allele ID (without accession) or the accession matches.
+near_matches() {
+    # Horrid REGEX, but we need to escape special chars and split the SEQID
+    local REGEX="$(echo "$1" |
+        sed -e 's,\([][().+?|*]\),\\\1,g' \
+            -e 's,^\([^_]*_[^_]*\)\(_.*\),^\1|\2$,')"
+    grep -E "$REGEX" | tr '\n' ' '
+}
+
+
+printf "
+===============================================================================
+I. Entries in phenotypes.txt with trailing whitespace in their identifier (col 1).
+   (This whitespace breaks simple key based lookups.)
+-------------------------------------------------------------------------------\n"
+cut -f1 phenotypes.txt | tail -n +2 | fgrep ' '
+
+
+printf "
+===============================================================================
+II. Entries in phenotypes.txt with no matching sequence in an *.fsa file.
+    Second column lists close matches (having identical alleleID or accession).
+-------------------------------------------------------------------------------\n"
+phenotype_ids | while read SEQID; do
+    sequence_ids | fgrep -xq "${SEQID}" ||
+        printf "$SEQID\t%s\n" "$(sequence_ids | near_matches "$SEQID")"
+done
+
+
+printf "
+===============================================================================
+III. Sequences in *.fsa that have no corresponding entry in phenotypes.txt.
+     Second column lists close matches (having identical alleleID or accession).
+-------------------------------------------------------------------------------\n"
+sequence_ids | while read SEQID; do
+    phenotype_ids | fgrep -xq "${SEQID}" ||
+        printf "$SEQID\t%s\n" "$(phenotype_ids | near_matches "$SEQID")"
+done
+
+# vim: sts=4:sw=4:si:et:ai