From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 2 Nov 2010 10:47:04 +0000 (+0000)
Subject: fixed bug in clip_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8edbc77f990ce55d6364d1beb2aa68a129677199;p=biopieces.git

fixed bug in clip_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1153 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/clip_seq b/bp_bin/clip_seq
index 4af564c..c2f9d8e 100755
--- a/bp_bin/clip_seq
+++ b/bp_bin/clip_seq
@@ -46,8 +46,11 @@ bp.each_record do |record|
 
     trim_beg = $`.length
 
-    record[:SEQ] =~ /[a-z]+$/
-    trim_end = $`.length
+    if record[:SEQ] =~ /[a-z]+$/
+      trim_end = $`.length
+    else
+      trim_end = record[:SEQ].length
+    end
 
     record[:SEQ]     = record[:SEQ][trim_beg ... trim_end]
     record[:SEQ_LEN] = record[:SEQ].length
diff --git a/bp_test/in/clip_seq.in b/bp_test/in/clip_seq.in
index 872d3fd..6a521d6 100644
--- a/bp_test/in/clip_seq.in
+++ b/bp_test/in/clip_seq.in
@@ -1,5 +1,20 @@
-SEQ_NAME: GP8WFI101DE0H9
+SEQ_NAME: test1
 SEQ: tcagTCTACGTCTCTGGACTGtaactgac
 SEQ_LEN: 29
 SCORES: hhhhhhhhhhTQQOSWZ^^XMMMNNS`YY
 ---
+SEQ_NAME: test2
+SEQ: TCTACGTCTCTGGACTGtaactgac
+SEQ_LEN: 25
+SCORES: hhhhhhTQQOSWZ^^XMMMNNS`YY
+---
+SEQ_NAME: test3
+SEQ: tcagTCTACGTCTCTGGACTG
+SEQ_LEN: 21
+SCORES: hhhhhhhhhhTQQOSWZ^^XM
+---
+SEQ_NAME: test4
+SEQ: TCTACGTCTCTGGACTG
+SEQ_LEN: 17
+SCORES: hhhhhhTQQOSWZ^^XM
+---
diff --git a/bp_test/out/clip_seq.out.1 b/bp_test/out/clip_seq.out.1
index bc97e94..c5ae7bd 100644
--- a/bp_test/out/clip_seq.out.1
+++ b/bp_test/out/clip_seq.out.1
@@ -1,4 +1,19 @@
-SEQ_NAME: GP8WFI101DE0H9
+SEQ_NAME: test1
+SEQ: TCTACGTCTCTGGACTG
+SEQ_LEN: 17
+SCORES: hhhhhhTQQOSWZ^^XM
+---
+SEQ_NAME: test2
+SEQ: TCTACGTCTCTGGACTG
+SEQ_LEN: 17
+SCORES: hhhhhhTQQOSWZ^^XM
+---
+SEQ_NAME: test3
+SEQ: TCTACGTCTCTGGACTG
+SEQ_LEN: 17
+SCORES: hhhhhhTQQOSWZ^^XM
+---
+SEQ_NAME: test4
 SEQ: TCTACGTCTCTGGACTG
 SEQ_LEN: 17
 SCORES: hhhhhhTQQOSWZ^^XM