added testing suite

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1017 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/align_seq.in b/bp_test/in/align_seq.in
new file mode 100644 (file)
index 0000000..aa030ba
--- /dev/null
+++ b/bp_test/in/align_seq.in
@@ -0,0 +1,20 @@
+SEQ: CTAGCTTCGACT
+SEQ_LEN: 12
+SEQ_NAME: test1
+---
+SEQ: GAATCGACT
+SEQ_LEN: 9
+SEQ_NAME: test2
+---
+SEQ: ACGAAACTAGCATC
+SEQ_LEN: 14
+SEQ_NAME: test3
+---
+SEQ: AGCATCGACT
+SEQ_LEN: 10
+SEQ_NAME: test4
+---
+SEQ: TAACAGGCACT
+SEQ_LEN: 11
+SEQ_NAME: test5
+---

diff --git a/bp_test/in/grab.in b/bp_test/in/grab.in
new file mode 100644 (file)
index 0000000..415979e
--- /dev/null
+++ b/bp_test/in/grab.in
@@ -0,0 +1,13 @@
+SEQ_NAME: test1
+SEQ_LEN: 10
+SEQ: MDESEQATHP
+---
+SEQ_NAME: test2
+SEQ_LEN: 8
+SEQ: ATCGatcg
+---
+PAT_NAME: test2
+PAT: SEQ
+---
+COUNT: 3
+---

diff --git a/bp_test/in/grab.in.pat b/bp_test/in/grab.in.pat
new file mode 100644 (file)
index 0000000..77ca6dd
--- /dev/null
+++ b/bp_test/in/grab.in.pat
@@ -0,0 +1,2 @@
+SEQ
+COUNT

diff --git a/bp_test/in/read_fasta.in b/bp_test/in/read_fasta.in
new file mode 100644 (file)
index 0000000..00beff4
--- /dev/null
+++ b/bp_test/in/read_fasta.in
@@ -0,0 +1,4 @@
+>test1
+ATCG
+>test2
+atcg

diff --git a/bp_test/in/write_fasta.in b/bp_test/in/write_fasta.in
new file mode 100644 (file)
index 0000000..6dcdf61
--- /dev/null
+++ b/bp_test/in/write_fasta.in
@@ -0,0 +1,4 @@
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test
+---

diff --git a/bp_test/lib/test.sh b/bp_test/lib/test.sh
new file mode 100755 (executable)
index 0000000..e753003
--- /dev/null
+++ b/bp_test/lib/test.sh
@@ -0,0 +1,47 @@
+#!/usr/bin/env sh
+
+bp=`basename $0 | sed s/^test_//`
+in="$BP_DIR/bp_test/in/$bp.in"
+out="$BP_DIR/bp_test/out/$bp.out"
+tmp="$BP_TMP/$bp.out"
+log_file="$BP_TMP/test.log"
+
+function run
+{
+    local command=$1
+
+    echo -n "Testing $command ... "
+    eval $command > /dev/null 2>&1
+}
+
+
+function assert_no_diff
+{
+    local src=$1
+    local dst=$2
+
+    local diff=`diff -q $src $dst`
+     
+    if [ "$diff" != "" ]; then
+        echo_red "FAIL"
+        echo "FAIL" >> $log_file
+    else     
+        echo_green "OK"
+        echo "OK" >> $log_file
+    fi     
+}
+
+
+function echo_green
+{
+    local msg=$1
+
+    echo -e "\033[32;38m$msg\033[0m"
+}
+
+function echo_red
+{
+    local msg=$1
+
+    echo -e "\033[31;38m$msg\033[0m"
+}

diff --git a/bp_test/out/align_seq.out.1 b/bp_test/out/align_seq.out.1
new file mode 100644 (file)
index 0000000..e161ba7
--- /dev/null
+++ b/bp_test/out/align_seq.out.1
@@ -0,0 +1,20 @@
+SEQ: ---TAACAGGCACT
+SEQ_LEN: 14
+SEQ_NAME: test5
+---
+SEQ: -----GAATCGACT
+SEQ_LEN: 14
+SEQ_NAME: test2
+---
+SEQ: --CTAGCTTCGACT
+SEQ_LEN: 14
+SEQ_NAME: test1
+---
+SEQ: ACGAAACTAGCATC
+SEQ_LEN: 14
+SEQ_NAME: test3
+---
+SEQ: ----AGCATCGACT
+SEQ_LEN: 14
+SEQ_NAME: test4
+---

diff --git a/bp_test/out/grab.out.1 b/bp_test/out/grab.out.1
new file mode 100644 (file)
index 0000000..5ffd399
--- /dev/null
+++ b/bp_test/out/grab.out.1
@@ -0,0 +1,11 @@
+SEQ: MDESEQATHP
+SEQ_LEN: 10
+SEQ_NAME: test1
+---
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test2
+---
+PAT: SEQ
+PAT_NAME: test2
+---

diff --git a/bp_test/out/grab.out.10 b/bp_test/out/grab.out.10
new file mode 100644 (file)
index 0000000..e117dbf
--- /dev/null
+++ b/bp_test/out/grab.out.10
@@ -0,0 +1,4 @@
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test2
+---

diff --git a/bp_test/out/grab.out.2 b/bp_test/out/grab.out.2
new file mode 100644 (file)
index 0000000..faac8b6
--- /dev/null
+++ b/bp_test/out/grab.out.2
@@ -0,0 +1,13 @@
+SEQ: MDESEQATHP
+SEQ_LEN: 10
+SEQ_NAME: test1
+---
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test2
+---
+PAT: SEQ
+PAT_NAME: test2
+---
+COUNT: 3
+---

diff --git a/bp_test/out/grab.out.3 b/bp_test/out/grab.out.3
new file mode 100644 (file)
index 0000000..faac8b6
--- /dev/null
+++ b/bp_test/out/grab.out.3
@@ -0,0 +1,13 @@
+SEQ: MDESEQATHP
+SEQ_LEN: 10
+SEQ_NAME: test1
+---
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test2
+---
+PAT: SEQ
+PAT_NAME: test2
+---
+COUNT: 3
+---

diff --git a/bp_test/out/grab.out.4 b/bp_test/out/grab.out.4
new file mode 100644 (file)
index 0000000..900f5c4
--- /dev/null
+++ b/bp_test/out/grab.out.4
@@ -0,0 +1,2 @@
+COUNT: 3
+---

diff --git a/bp_test/out/grab.out.5 b/bp_test/out/grab.out.5
new file mode 100644 (file)
index 0000000..67046b9
--- /dev/null
+++ b/bp_test/out/grab.out.5
@@ -0,0 +1,8 @@
+SEQ: MDESEQATHP
+SEQ_LEN: 10
+SEQ_NAME: test1
+---
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test2
+---

diff --git a/bp_test/out/grab.out.6 b/bp_test/out/grab.out.6
new file mode 100644 (file)
index 0000000..5bc1520
--- /dev/null
+++ b/bp_test/out/grab.out.6
@@ -0,0 +1,7 @@
+SEQ: MDESEQATHP
+SEQ_LEN: 10
+SEQ_NAME: test1
+---
+PAT: SEQ
+PAT_NAME: test2
+---

diff --git a/bp_test/out/grab.out.7 b/bp_test/out/grab.out.7
new file mode 100644 (file)
index 0000000..c60949d
--- /dev/null
+++ b/bp_test/out/grab.out.7
@@ -0,0 +1,3 @@
+PAT: SEQ
+PAT_NAME: test2
+---

diff --git a/bp_test/out/grab.out.8 b/bp_test/out/grab.out.8
new file mode 100644 (file)
index 0000000..e117dbf
--- /dev/null
+++ b/bp_test/out/grab.out.8
@@ -0,0 +1,4 @@
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test2
+---

diff --git a/bp_test/out/grab.out.9 b/bp_test/out/grab.out.9
new file mode 100644 (file)
index 0000000..67046b9
--- /dev/null
+++ b/bp_test/out/grab.out.9
@@ -0,0 +1,8 @@
+SEQ: MDESEQATHP
+SEQ_LEN: 10
+SEQ_NAME: test1
+---
+SEQ: ATCGatcg
+SEQ_LEN: 8
+SEQ_NAME: test2
+---

diff --git a/bp_test/out/read_fasta.out.1 b/bp_test/out/read_fasta.out.1
new file mode 100644 (file)
index 0000000..845ac01
--- /dev/null
+++ b/bp_test/out/read_fasta.out.1
@@ -0,0 +1,8 @@
+SEQ: ATCG
+SEQ_LEN: 4
+SEQ_NAME: test1
+---
+SEQ: atcg
+SEQ_LEN: 4
+SEQ_NAME: test2
+---

diff --git a/bp_test/out/read_fasta.out.2 b/bp_test/out/read_fasta.out.2
new file mode 100644 (file)
index 0000000..79b3251
--- /dev/null
+++ b/bp_test/out/read_fasta.out.2
@@ -0,0 +1,4 @@
+SEQ: ATCG
+SEQ_LEN: 4
+SEQ_NAME: test1
+---

diff --git a/bp_test/out/write_fasta.out.1 b/bp_test/out/write_fasta.out.1
new file mode 100644 (file)
index 0000000..0c4b8a8
--- /dev/null
+++ b/bp_test/out/write_fasta.out.1
@@ -0,0 +1,2 @@
+>test
+ATCGatcg

diff --git a/bp_test/out/write_fasta.out.2 b/bp_test/out/write_fasta.out.2
new file mode 100644 (file)
index 0000000..526b10c
--- /dev/null
+++ b/bp_test/out/write_fasta.out.2
@@ -0,0 +1,3 @@
+>test
+ATCG
+atcg

diff --git a/bp_test/test/test_align_seq b/bp_test/test/test_align_seq
new file mode 100755 (executable)
index 0000000..669747d
--- /dev/null
+++ b/bp_test/test/test_align_seq
@@ -0,0 +1,7 @@
+#!/usr/bin/env sh
+
+source "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_grab b/bp_test/test/test_grab
new file mode 100755 (executable)
index 0000000..bda9e3e
--- /dev/null
+++ b/bp_test/test/test_grab
@@ -0,0 +1,43 @@
+#!/usr/bin/env sh
+
+source "lib/test.sh"
+
+run "$bp -I $in -p SEQ -O $tmp.1"
+assert_no_diff $tmp.1 $out.1
+rm $tmp.1
+
+run "$bp -I $in -p SEQ,COUNT -O $tmp.2"
+assert_no_diff $tmp.2 $out.2
+rm $tmp.2
+
+run "$bp -I $in -P $in.pat -O $tmp.3"
+assert_no_diff $tmp.3 $out.3
+rm $tmp.3
+
+run "$bp -I $in -p SEQ -i -O $tmp.4"
+assert_no_diff $tmp.4 $out.4
+rm $tmp.4
+
+run "$bp -I $in -p SEQ -K -O $tmp.5"
+assert_no_diff $tmp.5 $out.5
+rm $tmp.5
+
+run "$bp -I $in -p SEQ -V -O $tmp.6"
+assert_no_diff $tmp.6 $out.6
+rm $tmp.6
+
+run "$bp -I $in -p SEQ -k PAT -O $tmp.7"
+assert_no_diff $tmp.7 $out.7
+rm $tmp.7
+
+run "$bp -I $in -r a -k SEQ -O $tmp.8"
+assert_no_diff $tmp.8 $out.8
+rm $tmp.8
+
+run "$bp -I $in -r a -k SEQ -c -O $tmp.9"
+assert_no_diff $tmp.9 $out.9
+rm $tmp.9
+
+run "$bp -I $in -e 'SEQ_LEN<10' -O $tmp.10"
+assert_no_diff $tmp.10 $out.10
+rm $tmp.10

diff --git a/bp_test/test/test_read_fasta b/bp_test/test/test_read_fasta
new file mode 100755 (executable)
index 0000000..aee8d00
--- /dev/null
+++ b/bp_test/test/test_read_fasta
@@ -0,0 +1,11 @@
+#!/usr/bin/env sh
+
+source "lib/test.sh"
+
+run "$bp -i $in -O $tmp.1"
+assert_no_diff $tmp.1 $out.1
+rm $tmp.1
+
+run "$bp -i $in -n 1 -O $tmp.2"
+assert_no_diff $tmp.2 $out.2
+rm $tmp.2

diff --git a/bp_test/test/test_write_fasta b/bp_test/test/test_write_fasta
new file mode 100755 (executable)
index 0000000..4597200
--- /dev/null
+++ b/bp_test/test/test_write_fasta
@@ -0,0 +1,11 @@
+#!/usr/bin/env sh
+
+source "lib/test.sh"
+
+run "write_fasta -I $in -o $tmp.1 -x"
+assert_no_diff $tmp.1 $out.1
+rm $tmp.1
+
+run "write_fasta -I $in -w 4 -o $tmp.2 -x"
+assert_no_diff $tmp.2 $out.2
+rm $tmp.2

diff --git a/bp_test/test_all b/bp_test/test_all
new file mode 100755 (executable)
index 0000000..061bec3
--- /dev/null
+++ b/bp_test/test_all
@@ -0,0 +1,29 @@
+#!/usr/bin/env sh
+
+source "lib/test.sh"
+
+rm $log_file
+
+count=0
+time0=`date +%s`
+
+for i in `ls "$BP_DIR/bp_test/test/"`; do
+    "$BP_DIR/bp_test/test/$i"
+    count=$[ $count + 1 ]
+done
+
+time1=`date +%s`
+time=$[ $time1 - $time0 ]
+
+test_count=`cat $log_file | wc -l | sed "s/ //g"`
+test_ok=`grep -c "OK" $log_file`
+
+test_fail=$[ $test_count - $test_ok ]
+
+report="Biopieces tested: $count   Tests run: $test_count   OK: $test_ok   FAIL: $test_fail   Time: $time secs"
+
+if [ $test_fail = 0 ]; then
+    echo_green "$report"
+else
+    echo_red "$report"
+fi