From 2d901e7bc53f21583f2585a0eec1b3180af97f36 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 20 Sep 2010 08:40:00 +0000
Subject: [PATCH] fixes and test for digest_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1096 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/digest_seq            |  4 ++--
 bp_test/in/digest_seq.in     |  4 ++++
 bp_test/out/digest_seq.out.1 | 10 ++++++++++
 bp_test/out/digest_seq.out.2 |  5 +++++
 bp_test/out/digest_seq.out.3 |  5 +++++
 bp_test/out/digest_seq.out.4 |  5 +++++
 bp_test/test/test_digest_seq | 19 +++++++++++++++++++
 code_ruby/Maasha/lib/seq.rb  | 13 ++++++++-----
 8 files changed, 58 insertions(+), 7 deletions(-)
 create mode 100644 bp_test/in/digest_seq.in
 create mode 100644 bp_test/out/digest_seq.out.1
 create mode 100644 bp_test/out/digest_seq.out.2
 create mode 100644 bp_test/out/digest_seq.out.3
 create mode 100644 bp_test/out/digest_seq.out.4
 create mode 100755 bp_test/test/test_digest_seq

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index 3fab531..34aebf0 100755
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -42,8 +42,6 @@ bp = Biopieces.new
 options = bp.parse(ARGV, casts)
 
 bp.each_record do |record|
-  bp.puts record
-
   if record.has_key? :SEQ_NAME and record.has_key? :SEQ
     seq    = Seq.new(record[:SEQ_NAME], record[:SEQ])
     digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
@@ -53,6 +51,8 @@ bp.each_record do |record|
       new_record[:REC_TYPE] = "DIGEST"
       bp.puts new_record
     end
+  else
+    bp.puts record
   end
 end
 
diff --git a/bp_test/in/digest_seq.in b/bp_test/in/digest_seq.in
new file mode 100644
index 0000000..6625cac
--- /dev/null
+++ b/bp_test/in/digest_seq.in
@@ -0,0 +1,4 @@
+SEQ_NAME: test
+SEQ: cgatcgatcGGATCCgagagggtgtgtagtgGAATTCcgctgc
+SEQ_LEN: 43
+---
diff --git a/bp_test/out/digest_seq.out.1 b/bp_test/out/digest_seq.out.1
new file mode 100644
index 0000000..5b099af
--- /dev/null
+++ b/bp_test/out/digest_seq.out.1
@@ -0,0 +1,10 @@
+SEQ_NAME: test[1-10]
+SEQ: cgatcgatcG
+SEQ_LEN: 10
+REC_TYPE: DIGEST
+---
+SEQ_NAME: test[11-43]
+SEQ: GATCCgagagggtgtgtagtgGAATTCcgctgc
+SEQ_LEN: 33
+REC_TYPE: DIGEST
+---
diff --git a/bp_test/out/digest_seq.out.2 b/bp_test/out/digest_seq.out.2
new file mode 100644
index 0000000..9f706c7
--- /dev/null
+++ b/bp_test/out/digest_seq.out.2
@@ -0,0 +1,5 @@
+SEQ_NAME: test[1-43]
+SEQ: cgatcgatcGGATCCgagagggtgtgtagtgGAATTCcgctgc
+SEQ_LEN: 43
+REC_TYPE: DIGEST
+---
diff --git a/bp_test/out/digest_seq.out.3 b/bp_test/out/digest_seq.out.3
new file mode 100644
index 0000000..9f706c7
--- /dev/null
+++ b/bp_test/out/digest_seq.out.3
@@ -0,0 +1,5 @@
+SEQ_NAME: test[1-43]
+SEQ: cgatcgatcGGATCCgagagggtgtgtagtgGAATTCcgctgc
+SEQ_LEN: 43
+REC_TYPE: DIGEST
+---
diff --git a/bp_test/out/digest_seq.out.4 b/bp_test/out/digest_seq.out.4
new file mode 100644
index 0000000..9f706c7
--- /dev/null
+++ b/bp_test/out/digest_seq.out.4
@@ -0,0 +1,5 @@
+SEQ_NAME: test[1-43]
+SEQ: cgatcgatcGGATCCgagagggtgtgtagtgGAATTCcgctgc
+SEQ_LEN: 43
+REC_TYPE: DIGEST
+---
diff --git a/bp_test/test/test_digest_seq b/bp_test/test/test_digest_seq
new file mode 100755
index 0000000..22082ac
--- /dev/null
+++ b/bp_test/test/test_digest_seq
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -p GGATCC -c 1 -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -p GGACTT -c 1 -I $in -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -p GGATCC -c 1000 -I $in -O $tmp"
+assert_no_diff $tmp $out.3
+clean
+
+run "$bp -p GGATCC -c -1000 -I $in -O $tmp"
+assert_no_diff $tmp $out.4
+clean
diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 8b98ace..2626ddc 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -168,13 +168,16 @@ class Digest
       @offset = pos + 1
     end
 
-    # Handle remaining sequence after last cut.
-    if @offset > 0 and @offset < @seq.seq.length
-      seq = Seq.new("#{@seq.seq_name}[#{@offset + 1}-#{@seq.seq.length}]", @seq.seq[@offset .. @seq.seq.length], @seq.type)
-
-      yield seq
+    if @offset < 0
+      @offset = 0
+    elsif @offset > @seq.seq.length
+      @offset = 0
     end
 
+    seq = Seq.new("#{@seq.seq_name}[#{@offset + 1}-#{@seq.seq.length}]", @seq.seq[@offset .. @seq.seq.length], @seq.type)
+
+    yield seq
+
     self # conventionally
   end
 
-- 
2.39.2