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 4af564c9b487467f65f441f54864f5ccad06509f..c2f9d8eb9fdebfeb2d724e64f79b63d140b3043e 100755 (executable)
--- 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 872d3fd3f74f6d525edb87c8bce446dc1c4c4392..6a521d646a3b5bd64f01b2b674be83734ef180ba 100644 (file)
--- 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 bc97e9455e8b7cfdf22567885ba6b97d77a0e702..c5ae7bdc70bac535cd5478ee5c409ab1ba312752 100644 (file)
--- 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