added cds/tools/compare

Former-commit-id: 07fb256bf17db3f0ffc1730b0383f8255fbb9129
Former-commit-id: fd6a1fe72a39c5633c2f9fb6de09af979c2a48f3

detectors/cds/tools/compare/lib/gbk.cds.awk

@@ -0,0 +1,84 @@
+#
+# get cds features from genbank (short version)
+#
+
+# @include lib.gbk.awk
+
+
+BEGIN {
+  if (MAXSPAN == "") MAXSPAN = 10000
+  print "#genefam gene from to strand nexon length status protseq product"
+}
+
+/^     CDS/ {
+  revstrand = match($2, "^complement")
+  s = substr($0, 22)
+  gsub("^complement", "", s)
+  ok = ! match(s, "complement|order")
+  nexon = Nexons(s)
+  SpanLocation(s, sloc)
+  spanlen = sloc[2] - sloc[1] + 1
+  len = LenLocation(s)
+  ok = ok && (len < MAXSPAN)
+  cdsseq = ok ? SeqLocation(seq, s, revstrand) : "XXX"
+  cstart = substr(cdsseq, 1,3)
+  cstop  = substr(cdsseq, length(cdsseq)-2)
+
+  gene = "none"
+  locustag = "none"
+  product = "none"
+  translation = "X"
+  incds = 1
+  next
+}
+
+(incds && /^     [^ ]/) {
+  print GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"), 
+        nexon, len, (ok ? "Ok" : "Error"), translation, product
+  incds = 0
+  next
+}
+
+/^                     \/gene=/ {
+  split($0, a, "=")
+  gene = a[2]
+  gsub("^[^a-z,A-Z]+", "", gene)
+  gsub("\"", "", gene)
+  gsub(" ", "_", gene)
+  next
+}
+
+/^                     \/locus_tag=/ {
+  split($0, a, "=")
+  locustag = a[2]
+  gsub("\"", "", locustag)
+  gsub(" ", "_", locustag)
+  next
+}
+
+/^                     \/product=/ {
+  split($0, a, "=")
+  product = a[2]
+  gsub("\"", "", product)
+  gsub(" ", "_", product)
+  next
+}
+
+/^                     \/translation=/ {
+  split($0, a, "=")
+  translation = a[2]
+  gsub("\"", "", translation)
+  gsub(" ", "", translation)
+  next
+}
+
+/^\/\// {
+  locus = "?"
+}
+
+END {
+  if (incds) {
+    print GeneFamily(gene), gene, sloc[1], sloc[2], (revstrand ? "R" : "D"), 
+          nexon, len, (ok ? "Ok" : "Error"), translation, product
+  }
+}