From be473361cd547ebfef8066b47c2fd0b2ff57b581 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Sat, 28 Dec 2013 13:22:35 -0800
Subject: [PATCH] add seq_to_grep

---
 seq_to_grep | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100755 seq_to_grep

diff --git a/seq_to_grep b/seq_to_grep
new file mode 100755
index 0000000..b88fdec
--- /dev/null
+++ b/seq_to_grep
@@ -0,0 +1,47 @@
+#!/usr/bin/perl
+
+# code	description
+# A	Adenine
+# C	Cytosine
+# G	Guanine
+# T	Thymine
+# U	Uracil
+# R	Purine (A or G)
+# Y	Pyrimidine (C, T, or U)
+# M	C or A
+# K	T, U, or G
+# W	T, U, or A
+# S	C or G
+# B	C, T, U, or G (not A)
+# D	A, T, U, or G (not C)
+# H	A, T, U, or C (not G)
+# V	A, C, or G (not T, not U)
+# N	Any base (A, C, G, T, or U)
+
+my %code_table =
+    (A => 'A',
+     C => 'C',
+     G => 'G',
+     T => 'TU',
+     U => 'TU',
+     R => 'AGR',
+     Y => 'CTUY',
+     M => 'CAM',
+     K => 'TUGK',
+     W => 'TUAW',
+     S => 'CGS',
+     B => 'CTUGBYWK',
+     D => 'ATUGDRWK',
+     H => 'ATUCHYWM',
+     V => 'ACGVRMS',
+     N => 'ACGTUYMKWSBDHVN',
+    );
+for my $code (keys %code_table) {
+    $code_table{$code} =
+        '['.$code_table{$code} . lc($code_table{$code}) .']';
+}
+
+for my $sequence (@ARGV) {
+    print map {exists $code_table{$_}?$code_table{$_}:$_} split //,$sequence;
+    print "\n";
+}
-- 
2.39.2