First version including the rRNA detector

Former-commit-id: 865e2626c7cd92ea596aedefe2b760b3eaaa9c77
Former-commit-id: 94a2e642328eb679660c6ac5a6cb6803c2083632

detectors/rrna/tools/revcomp_alignments.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+#
+#                   Reverse complement a fasta formated alignment
+#
+#========================================================================================
+
+# -- CAUTION -- Works as long than the script 
+#               is not called through a symlink
+SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
+source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
+
+
+function revcomp {
+    awk 'function printfasta(seq) {                                  \
+            seqlen=length(seq);                                       \
+            for (i=1; i <= seqlen; i+=60)                              \
+              print substr(seq,i,60);                                 \
+         }                                                          \
+        function comp(seq) {                                           \
+            "echo "seq" | tr acgtACGT tgcaTGCA " | getline res;     \
+            close("echo "seq" | tr acgtACGT tgcaTGCA "); \
+            return res;                                                \
+        }                                                              \
+        function rev(seq) {                                            \
+            "echo "seq" | rev " | getline res;                         \
+            close("echo "seq" | rev ");                                \
+            return res;                                                \
+        }                                                              \
+        function revcomp(seq) {                                        \
+            res=rev(comp(seq));                                        \
+            return res;                                                \
+        }                                                              \
+                                                                       \
+        (seq) && /^>/ {print head;                                     \
+                       printfasta(revcomp(seq));                       \
+                       seq=""}                                         \
+        /^>/   {head=$0}                                               \
+        ! /^>/ {seq=seq$0}                                             \
+        END { print head;                                     \
+              printfasta(revcomp(seq));                       \
+            }' $*
+}
+
+revcomp $*