added cat_seq biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1460 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/cat_seq b/bp_bin/cat_seq
new file mode 100755 (executable)
index 0000000..060b7d5
--- /dev/null
+++ b/bp_bin/cat_seq
@@ -0,0 +1,56 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Concatenates sequences in the stream and outputs a record with this sequence.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+require 'maasha/biopieces'
+
+options = Biopieces.options_parse(ARGV)
+
+seq = ""
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    seq << record[:SEQ] if record.has_key? :SEQ
+    output.puts record
+  end
+
+  new_record            = {}
+  new_record[:SEQ]      = seq
+  new_record[:SEQ_LEN]  = seq.length
+  new_record[:REC_TYPE] = "CAT"
+
+  output.puts new_record
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_test/in/cat_seq.in b/bp_test/in/cat_seq.in
new file mode 100644 (file)
index 0000000..1f6246f
--- /dev/null
+++ b/bp_test/in/cat_seq.in
@@ -0,0 +1,12 @@
+SEQ_NAME: test1
+SEQ: TACGATGCTAGCNATCYGACNACTGACTGACN
+SEQ_LEN: 32
+---
+SEQ_NAME: test2
+SEQ: TACGATGCTAGCNATCYGACNACTG
+SEQ_LEN: 25
+---
+SEQ_NAME: test3
+SEQ: TACGATGCTAGCNATCY
+SEQ_LEN: 17
+---

diff --git a/bp_test/out/cat_seq.out.1 b/bp_test/out/cat_seq.out.1
new file mode 100644 (file)
index 0000000..45481e8
--- /dev/null
+++ b/bp_test/out/cat_seq.out.1
@@ -0,0 +1,16 @@
+SEQ_NAME: test1
+SEQ: TACGATGCTAGCNATCYGACNACTGACTGACN
+SEQ_LEN: 32
+---
+SEQ_NAME: test2
+SEQ: TACGATGCTAGCNATCYGACNACTG
+SEQ_LEN: 25
+---
+SEQ_NAME: test3
+SEQ: TACGATGCTAGCNATCY
+SEQ_LEN: 17
+---
+SEQ: TACGATGCTAGCNATCYGACNACTGACTGACNTACGATGCTAGCNATCYGACNACTGTACGATGCTAGCNATCY
+SEQ_LEN: 74
+REC_TYPE: CAT
+---

diff --git a/bp_test/test/test_cat_seq b/bp_test/test/test_cat_seq
new file mode 100755 (executable)
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_cat_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