From a949711879aa421a6e36c4b7f34305525d64a585 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 6 Jun 2011 15:21:33 +0000
Subject: [PATCH] fixed cat_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1462 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/cat_seq            |  9 +++++++--
 bp_test/out/cat_seq.out.1 |  1 +
 bp_test/out/cat_seq.out.2 |  5 +++++
 bp_test/out/cat_seq.out.3 | 17 +++++++++++++++++
 bp_test/test/test_cat_seq |  8 ++++++++
 5 files changed, 38 insertions(+), 2 deletions(-)
 create mode 100644 bp_test/out/cat_seq.out.2
 create mode 100644 bp_test/out/cat_seq.out.3

diff --git a/bp_bin/cat_seq b/bp_bin/cat_seq
index 060b7d5..88e9d24 100755
--- a/bp_bin/cat_seq
+++ b/bp_bin/cat_seq
@@ -31,17 +31,22 @@
 
 require 'maasha/biopieces'
 
-options = Biopieces.options_parse(ARGV)
+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.has_key? :SEQ
-    output.puts record
+    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"
diff --git a/bp_test/out/cat_seq.out.1 b/bp_test/out/cat_seq.out.1
index 45481e8..b616ca7 100644
--- a/bp_test/out/cat_seq.out.1
+++ b/bp_test/out/cat_seq.out.1
@@ -10,6 +10,7 @@ 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
new file mode 100644
index 0000000..36b89c6
--- /dev/null
+++ b/bp_test/out/cat_seq.out.2
@@ -0,0 +1,5 @@
+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
new file mode 100644
index 0000000..56f5610
--- /dev/null
+++ b/bp_test/out/cat_seq.out.3
@@ -0,0 +1,17 @@
+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
index 61c5709..a508434 100755
--- a/bp_test/test/test_cat_seq
+++ b/bp_test/test/test_cat_seq
@@ -5,3 +5,11 @@ 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