combine gtdb and user data

Author: yazhinia

unifygtdb.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+# Usage: bash unify.sh gtdb_taxonomy.tsv gtdbtk_species_representatives.tsv memberships.tsv > unified.tsv
+
+GTDB_TAX="$1"
+GTDBTK="$2"
+MEMBERS="$3"
+
+awk '
+BEGIN { OFS="\t"; print "#user_representative\tgtdb_representative" }
+
+# File 1: gtdb_taxonomy.tsv -> species -> GTDB reference genome
+FILENAME==ARGV[1] {
+    if ($0 ~ /^#/) next
+    genome = $1
+    split($0, a, "s__")
+    species = a[length(a)]
+    if (species != "" && !(species in gtdb_ref))
+        gtdb_ref[species] = genome
+    gtdb_species[species] = 1
+    next
+}
+
+# File 2: gtdbtk_species_representatives.tsv -> your_rep -> species
+FILENAME==ARGV[2] {
+    if ($0 ~ /^#/) next
+    your_rep = $1
+    split($0, a, "s__")
+    species = a[length(a)]
+    bin_species[your_rep] = species
+    next
+}
+
+# File 3: memberships.tsv -> process each representative
+FILENAME==ARGV[3] {
+    if ($0 ~ /^#/) next
+    your_rep = $1
+    species = (your_rep in bin_species) ? bin_species[your_rep] : ""
+    if (species != "" && species in gtdb_ref) {
+        print your_rep, gtdb_ref[species]   # user rep -> matched GTDB ref
+        covered[species] = 1
+    } else {
+        print your_rep, "unknown"           # no GTDB species match
+    }
+    next
+}
+
+END {
+    # GTDB species not covered by any user representative
+    for (species in gtdb_ref) {
+        if (!(species in covered)) {
+            ref = gtdb_ref[species]
+            print ref, ref
+        }
+    }
+}
+' "$GTDB_TAX" "$GTDBTK" "$MEMBERS"