From b0f2727000b3611af4b232ce71f86a577696eb88 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 8 Mar 2013 13:10:10 +0000
Subject: [PATCH] dropped cat_seq Biopieces since join_seq exists

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2118 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/cat_seq            | 61 ---------------------------------------
 bp_test/in/cat_seq.in     | 12 --------
 bp_test/out/cat_seq.out.1 | 17 -----------
 bp_test/out/cat_seq.out.2 |  5 ----
 bp_test/out/cat_seq.out.3 | 17 -----------
 bp_test/test/test_cat_seq | 15 ----------
 6 files changed, 127 deletions(-)
 delete mode 100755 bp_bin/cat_seq
 delete mode 100644 bp_test/in/cat_seq.in
 delete mode 100644 bp_test/out/cat_seq.out.1
 delete mode 100644 bp_test/out/cat_seq.out.2
 delete mode 100644 bp_test/out/cat_seq.out.3
 delete mode 100755 bp_test/test/test_cat_seq

diff --git a/bp_bin/cat_seq b/bp_bin/cat_seq
deleted file mode 100755
index 67cf397..0000000
--- a/bp_bin/cat_seq
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/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'
-
-casts = []
-casts << {:long=>'seq_name',  :short=>'s', :type=>'string', :mandatory=>true,  :default=>"cat_seq", :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,       :allowed=>nil, :disallowed=>nil}
-
-options = Biopieces.options_parse(ARGV, casts)
-
-seq = ""
-
-Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  input.each_record do |record|
-    seq << record[:SEQ] if record[:SEQ]
-    output.puts record unless options[:no_stream]
-  end
-
-  new_record            = {}
-  new_record[:SEQ_NAME] = options[:seq_name]
-  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
deleted file mode 100644
index 1f6246f..0000000
--- a/bp_test/in/cat_seq.in
+++ /dev/null
@@ -1,12 +0,0 @@
-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
deleted file mode 100644
index b616ca7..0000000
--- a/bp_test/out/cat_seq.out.1
+++ /dev/null
@@ -1,17 +0,0 @@
-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_NAME: cat_seq
-SEQ: TACGATGCTAGCNATCYGACNACTGACTGACNTACGATGCTAGCNATCYGACNACTGTACGATGCTAGCNATCY
-SEQ_LEN: 74
-REC_TYPE: CAT
----
diff --git a/bp_test/out/cat_seq.out.2 b/bp_test/out/cat_seq.out.2
deleted file mode 100644
index 36b89c6..0000000
--- a/bp_test/out/cat_seq.out.2
+++ /dev/null
@@ -1,5 +0,0 @@
-SEQ_NAME: cat_seq
-SEQ: TACGATGCTAGCNATCYGACNACTGACTGACNTACGATGCTAGCNATCYGACNACTGTACGATGCTAGCNATCY
-SEQ_LEN: 74
-REC_TYPE: CAT
----
diff --git a/bp_test/out/cat_seq.out.3 b/bp_test/out/cat_seq.out.3
deleted file mode 100644
index 56f5610..0000000
--- a/bp_test/out/cat_seq.out.3
+++ /dev/null
@@ -1,17 +0,0 @@
-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_NAME: Foobar
-SEQ: TACGATGCTAGCNATCYGACNACTGACTGACNTACGATGCTAGCNATCYGACNACTGTACGATGCTAGCNATCY
-SEQ_LEN: 74
-REC_TYPE: CAT
----
diff --git a/bp_test/test/test_cat_seq b/bp_test/test/test_cat_seq
deleted file mode 100755
index a508434..0000000
--- a/bp_test/test/test_cat_seq
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-source "$BP_DIR/bp_test/lib/test.sh"
-
-run "$bp -I $in -O $tmp"
-assert_no_diff $tmp $out.1
-clean
-
-run "$bp -I $in -x -O $tmp"
-assert_no_diff $tmp $out.2
-clean
-
-run "$bp -I $in -s Foobar -O $tmp"
-assert_no_diff $tmp $out.3
-clean
-- 
2.39.2