added clip_seq biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1152 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/clip_seq b/bp_bin/clip_seq
new file mode 100755 (executable)
index 0000000..4af564c
--- /dev/null
+++ b/bp_bin/clip_seq
@@ -0,0 +1,64 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Clip sequences in the stream based on soft masked sequence.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'biopieces'
+
+casts = []
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+bp.each_record do |record|
+  if record.has_key? :SEQ
+    trim_beg = 0
+    trim_end = record[:SEQ].length
+
+    record[:SEQ] =~ /[^a-z]/
+
+    trim_beg = $`.length
+
+    record[:SEQ] =~ /[a-z]+$/
+    trim_end = $`.length
+
+    record[:SEQ]     = record[:SEQ][trim_beg ... trim_end]
+    record[:SEQ_LEN] = record[:SEQ].length
+    record[:SCORES]  = record[:SCORES][trim_beg ... trim_end] if record.has_key? :SCORES
+  end
+
+  bp.puts record
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_test/in/clip_seq.in b/bp_test/in/clip_seq.in
new file mode 100644 (file)
index 0000000..872d3fd
--- /dev/null
+++ b/bp_test/in/clip_seq.in
@@ -0,0 +1,5 @@
+SEQ_NAME: GP8WFI101DE0H9
+SEQ: tcagTCTACGTCTCTGGACTGtaactgac
+SEQ_LEN: 29
+SCORES: hhhhhhhhhhTQQOSWZ^^XMMMNNS`YY
+---

diff --git a/bp_test/out/clip_seq.out.1 b/bp_test/out/clip_seq.out.1
new file mode 100644 (file)
index 0000000..bc97e94
--- /dev/null
+++ b/bp_test/out/clip_seq.out.1
@@ -0,0 +1,5 @@
+SEQ_NAME: GP8WFI101DE0H9
+SEQ: TCTACGTCTCTGGACTG
+SEQ_LEN: 17
+SCORES: hhhhhhTQQOSWZ^^XM
+---

diff --git a/bp_test/test/test_clip_seq b/bp_test/test/test_clip_seq
new file mode 100755 (executable)
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_clip_seq
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean