added base36.rb Ruby library

[biopieces.git] / bp_bin / find_mids

diff --git a/bp_bin/find_mids b/bp_bin/find_mids
index b02048b1d73938be770b19d0fd3615ad34729ff0..4e6104975f1da424d655b85e664861dd1b2a2bef 100755 (executable)
--- a/bp_bin/find_mids
+++ b/bp_bin/find_mids
@@ -24,7 +24,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-#
+# Find and count MID tags in sequences in the stream.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -62,9 +62,12 @@ mids = %w{ ACGAGTGCGT ACGCTCGACA AGACGCACTC AGCACTGTAG ATCAGACACG
            CTATGTACAG CTCGATATAG CTCGCACGCG CTGCGTCACG CTGTGCGTCG
            TAGCATACTG TATACATGTG TATCACTCAG TATCTGATAG TCGTGACATG
            TCTGATCGAG TGACATCTCG TGAGCTAGAG TGATAGAGCG TGCGTGTGCG
-           TGCTAGTCAG TGTATCACAG TGTGCGCGTG
+           TGCTAGTCAG TGTATCACAG TGTGCGCGTG ACACGACGAC ACACGTAGTA
+           ACACTACTCG ACGACACGTA ACGAGTAGAC ACGCGTCTAG ACGTACACAC
+           ACGTACTGTG ACGTAGATCG ACTACGTCTC ACTATACGAG ACTCGCGTCG
 }
 
+
 count_hash = Hash.new { |hash, key| hash[key] = 0 }
 mid_hash   = {}
 
@@ -80,8 +83,10 @@ options = bp.parse(ARGV, casts)
 
 bp.each_record do |record|
   if record.has_key? :SEQ
-    if mid_hash.has_key? record[:SEQ][4 ... 14]
-      count_hash[record[:SEQ][4 ... 14]] += 1
+    tag = record[:SEQ][4 ... 14].upcase
+
+    if mid_hash.has_key? tag
+      count_hash[tag] += 1
     end
   end
   bp.puts record