diff utils/msa2fa.awk @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils/msa2fa.awk	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,22 @@
+# A quick script to convert the .msa.tsv output of sscs.py back into FASTA format.
+
+BEGIN {
+  FS = "\t";
+  OFS = "\t";
+}
+
+$2 == "CONSENSUS" {
+  if ($1 == last) {
+    mate = 2;
+  } else {
+    mate = 1;
+  }
+  printf(">%s.%d:%d\n", $1, mate, pairs);
+  print $3;
+  pairs = 0;
+  last = $1;
+}
+
+$2 != "CONSENSUS" {
+  pairs++;
+}
\ No newline at end of file