added more tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1026 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/lowercase_seq.in b/bp_test/in/lowercase_seq.in
new file mode 100644 (file)
index 0000000..bfa9ff1
--- /dev/null
+++ b/bp_test/in/lowercase_seq.in
@@ -0,0 +1,2 @@
+SEQ: ATCG
+---

diff --git a/bp_test/in/read_tab.in.1 b/bp_test/in/read_tab.in.1
new file mode 100644 (file)
index 0000000..70aba61
--- /dev/null
+++ b/bp_test/in/read_tab.in.1
@@ -0,0 +1,5 @@
+Organism   Sequence    Count
+Human      ATACGTCAG   23524
+Dog        AGCATGAC    2442
+Mouse      GACTG       234
+Cat        AAATGCA     2342

diff --git a/bp_test/in/read_tab.in.2 b/bp_test/in/read_tab.in.2
new file mode 100644 (file)
index 0000000..28af0cb
--- /dev/null
+++ b/bp_test/in/read_tab.in.2
@@ -0,0 +1,5 @@
+#Organism   Sequence    Count
+Human      ATACGTCAG   23524
+Dog        AGCATGAC    2442
+Mouse      GACTG       234
+Cat        AAATGCA     2342

diff --git a/bp_test/in/read_tab.in.3 b/bp_test/in/read_tab.in.3
new file mode 100644 (file)
index 0000000..6456ebd
--- /dev/null
+++ b/bp_test/in/read_tab.in.3
@@ -0,0 +1,5 @@
+#Organism;Sequence;Count
+Human;ATACGTCAG;23524
+Dog;AGCATGAC;2442
+Mouse;GACTG;234
+Cat;AAATGCA;2342

diff --git a/bp_test/in/uppercase_seq.in b/bp_test/in/uppercase_seq.in
new file mode 100644 (file)
index 0000000..b284b95
--- /dev/null
+++ b/bp_test/in/uppercase_seq.in
@@ -0,0 +1,2 @@
+SEQ: atcg
+---

diff --git a/bp_test/out/lowercase_seq.out.1 b/bp_test/out/lowercase_seq.out.1
new file mode 100644 (file)
index 0000000..b284b95
--- /dev/null
+++ b/bp_test/out/lowercase_seq.out.1
@@ -0,0 +1,2 @@
+SEQ: atcg
+---

diff --git a/bp_test/out/read_tab.out.1 b/bp_test/out/read_tab.out.1
new file mode 100644 (file)
index 0000000..0ccc0a1
--- /dev/null
+++ b/bp_test/out/read_tab.out.1
@@ -0,0 +1,20 @@
+V0: Organism
+V2: Count
+V1: Sequence
+---
+V0: Human
+V2: 23524
+V1: ATACGTCAG
+---
+V0: Dog
+V2: 2442
+V1: AGCATGAC
+---
+V0: Mouse
+V2: 234
+V1: GACTG
+---
+V0: Cat
+V2: 2342
+V1: AAATGCA
+---

diff --git a/bp_test/out/read_tab.out.2 b/bp_test/out/read_tab.out.2
new file mode 100644 (file)
index 0000000..5cffc52
--- /dev/null
+++ b/bp_test/out/read_tab.out.2
@@ -0,0 +1,16 @@
+V0: Human
+V2: 23524
+V1: ATACGTCAG
+---
+V0: Dog
+V2: 2442
+V1: AGCATGAC
+---
+V0: Mouse
+V2: 234
+V1: GACTG
+---
+V0: Cat
+V2: 2342
+V1: AAATGCA
+---

diff --git a/bp_test/out/read_tab.out.3 b/bp_test/out/read_tab.out.3
new file mode 100644 (file)
index 0000000..dc0f6c3
--- /dev/null
+++ b/bp_test/out/read_tab.out.3
@@ -0,0 +1,16 @@
+SEQ: ATACGTCAG
+ORGANISM: Human
+COUNT: 23524
+---
+SEQ: AGCATGAC
+ORGANISM: Dog
+COUNT: 2442
+---
+SEQ: GACTG
+ORGANISM: Mouse
+COUNT: 234
+---
+SEQ: AAATGCA
+ORGANISM: Cat
+COUNT: 2342
+---

diff --git a/bp_test/out/read_tab.out.4 b/bp_test/out/read_tab.out.4
new file mode 100644 (file)
index 0000000..113db41
--- /dev/null
+++ b/bp_test/out/read_tab.out.4
@@ -0,0 +1,12 @@
+V0: 23524
+V1: ATACGTCAG
+---
+V0: 2442
+V1: AGCATGAC
+---
+V0: 234
+V1: GACTG
+---
+V0: 2342
+V1: AAATGCA
+---

diff --git a/bp_test/out/read_tab.out.5 b/bp_test/out/read_tab.out.5
new file mode 100644 (file)
index 0000000..04520e6
--- /dev/null
+++ b/bp_test/out/read_tab.out.5
@@ -0,0 +1,12 @@
+SEQ: ATACGTCAG
+COUNT: 23524
+---
+SEQ: AGCATGAC
+COUNT: 2442
+---
+SEQ: GACTG
+COUNT: 234
+---
+SEQ: AAATGCA
+COUNT: 2342
+---

diff --git a/bp_test/out/read_tab.out.6 b/bp_test/out/read_tab.out.6
new file mode 100644 (file)
index 0000000..00a3fdf
--- /dev/null
+++ b/bp_test/out/read_tab.out.6
@@ -0,0 +1,16 @@
+Organism: Human
+Count: 23524
+Sequence: ATACGTCAG
+---
+Organism: Dog
+Count: 2442
+Sequence: AGCATGAC
+---
+Organism: Mouse
+Count: 234
+Sequence: GACTG
+---
+Organism: Cat
+Count: 2342
+Sequence: AAATGCA
+---

diff --git a/bp_test/out/read_tab.out.7 b/bp_test/out/read_tab.out.7
new file mode 100644 (file)
index 0000000..5363c4a
--- /dev/null
+++ b/bp_test/out/read_tab.out.7
@@ -0,0 +1,4 @@
+Organism: Human
+Count: 23524
+Sequence: ATACGTCAG
+---

diff --git a/bp_test/out/read_tab.out.8 b/bp_test/out/read_tab.out.8
new file mode 100644 (file)
index 0000000..00a3fdf
--- /dev/null
+++ b/bp_test/out/read_tab.out.8
@@ -0,0 +1,16 @@
+Organism: Human
+Count: 23524
+Sequence: ATACGTCAG
+---
+Organism: Dog
+Count: 2442
+Sequence: AGCATGAC
+---
+Organism: Mouse
+Count: 234
+Sequence: GACTG
+---
+Organism: Cat
+Count: 2342
+Sequence: AAATGCA
+---

diff --git a/bp_test/out/uppercase_seq.out.1 b/bp_test/out/uppercase_seq.out.1
new file mode 100644 (file)
index 0000000..bfa9ff1
--- /dev/null
+++ b/bp_test/out/uppercase_seq.out.1
@@ -0,0 +1,2 @@
+SEQ: ATCG
+---

diff --git a/bp_test/test/test_lowercase_seq b/bp_test/test/test_lowercase_seq
new file mode 100755 (executable)
index 0000000..3f4ad21
--- /dev/null
+++ b/bp_test/test/test_lowercase_seq
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp.1"
+assert_no_diff $tmp.1 $out.1
+rm $tmp.1

diff --git a/bp_test/test/test_read_tab b/bp_test/test/test_read_tab
new file mode 100755 (executable)
index 0000000..f1c73c8
--- /dev/null
+++ b/bp_test/test/test_read_tab
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -i $in.1 -O $tmp.1"
+assert_no_diff $tmp.1 $out.1
+rm $tmp.1
+
+run "$bp -i $in.1 -s 1 -O $tmp.2"
+assert_no_diff $tmp.2 $out.2
+rm $tmp.2
+
+run "$bp -i $in.1 -s 1 -k ORGANISM,SEQ,COUNT -O $tmp.3"
+assert_no_diff $tmp.3 $out.3
+rm $tmp.3
+
+run "$bp -i $in.1 -s 1 -c 2,1 -O $tmp.4"
+assert_no_diff $tmp.4 $out.4
+rm $tmp.4
+
+run "$bp -i $in.1 -s 1 -c 2,1 -k COUNT,SEQ -O $tmp.5"
+assert_no_diff $tmp.5 $out.5
+rm $tmp.5
+
+run "$bp -i $in.2 -O $tmp.6"
+assert_no_diff $tmp.6 $out.6
+rm $tmp.6
+
+run "$bp -i $in.2 -n 1 -O $tmp.7"
+assert_no_diff $tmp.7 $out.7
+rm $tmp.7
+
+run "$bp -i $in.3 -d ';' -O $tmp.8"
+assert_no_diff $tmp.8 $out.8
+rm $tmp.8

diff --git a/bp_test/test/test_uppercase_seq b/bp_test/test/test_uppercase_seq
new file mode 100755 (executable)
index 0000000..3f4ad21
--- /dev/null
+++ b/bp_test/test/test_uppercase_seq
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp.1"
+assert_no_diff $tmp.1 $out.1
+rm $tmp.1