added tests for create_seq_index and get_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2075 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/create_seq_index.in b/bp_test/in/create_seq_index.in
new file mode 100644 (file)
index 0000000..df3ae4c
--- /dev/null
+++ b/bp_test/in/create_seq_index.in
@@ -0,0 +1,11 @@
+SEQ_NAME: test1
+SEQ: AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT
+SEQ_LEN: 100
+---
+SEQ_NAME: test2
+SEQ: TGGGCGTTCAGGTAAATAGGCGTGTGAATTTAAATAACGAGTGGTGATGCCTTGTATAACACCCTATATTCGTTCTCGAATGTCCGACGTACTATAACGT
+SEQ_LEN: 100
+---
+SEQ_NAME: test3
+SEQ: ATAGTACTACAGTAACGAAAGTCGTGGTTGTATCTCCTTTATGGCCGGTCGTTGGGAATTAAAGACTCCACGTAGACGACGATTTTTCTGAAGAGCTTTA
+SEQ_LEN: 100

diff --git a/bp_test/in/get_seq.in.1 b/bp_test/in/get_seq.in.1
new file mode 100644 (file)
index 0000000..df3ae4c
--- /dev/null
+++ b/bp_test/in/get_seq.in.1
@@ -0,0 +1,11 @@
+SEQ_NAME: test1
+SEQ: AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT
+SEQ_LEN: 100
+---
+SEQ_NAME: test2
+SEQ: TGGGCGTTCAGGTAAATAGGCGTGTGAATTTAAATAACGAGTGGTGATGCCTTGTATAACACCCTATATTCGTTCTCGAATGTCCGACGTACTATAACGT
+SEQ_LEN: 100
+---
+SEQ_NAME: test3
+SEQ: ATAGTACTACAGTAACGAAAGTCGTGGTTGTATCTCCTTTATGGCCGGTCGTTGGGAATTAAAGACTCCACGTAGACGACGATTTTTCTGAAGAGCTTTA
+SEQ_LEN: 100

diff --git a/bp_test/in/get_seq.in.2 b/bp_test/in/get_seq.in.2
new file mode 100644 (file)
index 0000000..bfd9f4d
--- /dev/null
+++ b/bp_test/in/get_seq.in.2
@@ -0,0 +1,12 @@
+BEG: 5
+LEN: 5
+SEQ_NAME: test1
+---
+BEG: 7
+LEN: 5
+SEQ_NAME: test2
+---
+BEG: 9
+LEN: 5
+SEQ_NAME: test3
+---

diff --git a/bp_test/out/create_seq_index.out.1 b/bp_test/out/create_seq_index.out.1
new file mode 100644 (file)
index 0000000..da72f28
--- /dev/null
+++ b/bp_test/out/create_seq_index.out.1
@@ -0,0 +1,6 @@
+>test1
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT
+>test2
+TGGGCGTTCAGGTAAATAGGCGTGTGAATTTAAATAACGAGTGGTGATGCCTTGTATAACACCCTATATTCGTTCTCGAATGTCCGACGTACTATAACGT
+>test3
+ATAGTACTACAGTAACGAAAGTCGTGGTTGTATCTCCTTTATGGCCGGTCGTTGGGAATTAAAGACTCCACGTAGACGACGATTTTTCTGAAGAGCTTTA

diff --git a/bp_test/out/get_seq.out.1 b/bp_test/out/get_seq.out.1
new file mode 100644 (file)
index 0000000..bdd80f7
--- /dev/null
+++ b/bp_test/out/get_seq.out.1
@@ -0,0 +1,4 @@
+SEQ: TTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAAT
+SEQ_LEN: 91
+SEQ_NAME: test1
+---

diff --git a/bp_test/out/get_seq.out.2 b/bp_test/out/get_seq.out.2
new file mode 100644 (file)
index 0000000..c7cd278
--- /dev/null
+++ b/bp_test/out/get_seq.out.2
@@ -0,0 +1,4 @@
+SEQ: AGCTTTTCAT
+SEQ_LEN: 10
+SEQ_NAME: test1
+---

diff --git a/bp_test/out/get_seq.out.3 b/bp_test/out/get_seq.out.3
new file mode 100644 (file)
index 0000000..c7cd278
--- /dev/null
+++ b/bp_test/out/get_seq.out.3
@@ -0,0 +1,4 @@
+SEQ: AGCTTTTCAT
+SEQ_LEN: 10
+SEQ_NAME: test1
+---

diff --git a/bp_test/out/get_seq.out.4 b/bp_test/out/get_seq.out.4
new file mode 100644 (file)
index 0000000..a06c7da
--- /dev/null
+++ b/bp_test/out/get_seq.out.4
@@ -0,0 +1,4 @@
+SEQ: TTCTGACTGC
+SEQ_LEN: 10
+SEQ_NAME: test1
+---

diff --git a/bp_test/out/get_seq.out.5 b/bp_test/out/get_seq.out.5
new file mode 100644 (file)
index 0000000..0fef0a5
--- /dev/null
+++ b/bp_test/out/get_seq.out.5
@@ -0,0 +1,18 @@
+BEG: 5
+SEQ: TTCAT
+SEQ_LEN: 5
+SEQ_NAME: test1
+LEN: 5
+---
+BEG: 7
+SEQ: TCAGG
+SEQ_LEN: 5
+SEQ_NAME: test2
+LEN: 5
+---
+BEG: 9
+SEQ: CAGTA
+SEQ_LEN: 5
+SEQ_NAME: test3
+LEN: 5
+---

diff --git a/bp_test/test/test_create_seq_index b/bp_test/test/test_create_seq_index
new file mode 100755 (executable)
index 0000000..e35d5ae
--- /dev/null
+++ b/bp_test/test/test_create_seq_index
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -d $tmp_dir -i test -x"
+assert_no_diff "$tmp_dir/test.seq" $out.1
+clean
+
+rm -rf $tmp_dir

diff --git a/bp_test/test/test_get_seq b/bp_test/test/test_get_seq
new file mode 100755 (executable)
index 0000000..ac70292
--- /dev/null
+++ b/bp_test/test/test_get_seq
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run_quiet "create_seq_index -I $in.1 -d $tmp_dir -i test -x"
+
+run "$bp -i $tmp_dir/test -s test1 -b 10 -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -i $tmp_dir/test -s test1 -e 10 -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -i $tmp_dir/test -s test1 -l 10 -O $tmp"
+assert_no_diff $tmp $out.3
+clean
+
+run "$bp -i $tmp_dir/test -s test1 -b 10 -l 10 -O $tmp"
+assert_no_diff $tmp $out.4
+clean
+
+run "$bp -I $in.2 -i $tmp_dir/test -O $tmp"
+assert_no_diff $tmp $out.5
+clean
+
+rm -rf $tmp_dir