polishing on testing suite

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1027 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/out/write_fasta.out.3 b/bp_test/out/write_fasta.out.3
new file mode 100644 (file)
index 0000000..3aa5067
Binary files /dev/null and b/bp_test/out/write_fasta.out.3 differ

diff --git a/bp_test/test/test_align_seq b/bp_test/test/test_align_seq
index 3f4ad21f730ced60ba7a07bbdaf6f852f9c00b5b..4266db8615e96094938fc886e5d4902d3ef70b56 100755 (executable)
--- a/bp_test/test/test_align_seq
+++ b/bp_test/test/test_align_seq
@@ -2,6 +2,6 @@
 
 source "$BP_DIR/bp_test/lib/test.sh"
 
-run "$bp -I $in -O $tmp.1"
-assert_no_diff $tmp.1 $out.1
-rm $tmp.1
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+rm $tmp

diff --git a/bp_test/test/test_grab b/bp_test/test/test_grab
index 75e12ac7aae7c09c9e3d7c50f96f7f6bff24df44..4d97be063b9155132296d4ec327d3f5142964b0b 100755 (executable)
--- a/bp_test/test/test_grab
+++ b/bp_test/test/test_grab
@@ -2,42 +2,42 @@
 
 source "$BP_DIR/bp_test/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 -O $tmp"
+assert_no_diff $tmp $out.1
+rm $tmp
 
-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 SEQ,COUNT -O $tmp"
+assert_no_diff $tmp $out.2
+rm $tmp
 
-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 $in.pat -O $tmp"
+assert_no_diff $tmp $out.3
+rm $tmp
 
-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 -i -O $tmp"
+assert_no_diff $tmp $out.4
+rm $tmp
 
-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 -K -O $tmp"
+assert_no_diff $tmp $out.5
+rm $tmp
 
-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 -V -O $tmp"
+assert_no_diff $tmp $out.6
+rm $tmp
 
-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 -p SEQ -k PAT -O $tmp"
+assert_no_diff $tmp $out.7
+rm $tmp
 
-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 -O $tmp"
+assert_no_diff $tmp $out.8
+rm $tmp
 
-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 -r a -k SEQ -c -O $tmp"
+assert_no_diff $tmp $out.9
+rm $tmp
 
-run "$bp -I $in -e 'SEQ_LEN<10' -O $tmp.10"
-assert_no_diff $tmp.10 $out.10
-rm $tmp.10
+run "$bp -I $in -e 'SEQ_LEN<10' -O $tmp"
+assert_no_diff $tmp $out.10
+rm $tmp

diff --git a/bp_test/test/test_lowercase_seq b/bp_test/test/test_lowercase_seq
index 3f4ad21f730ced60ba7a07bbdaf6f852f9c00b5b..4266db8615e96094938fc886e5d4902d3ef70b56 100755 (executable)
--- a/bp_test/test/test_lowercase_seq
+++ b/bp_test/test/test_lowercase_seq
@@ -2,6 +2,6 @@
 
 source "$BP_DIR/bp_test/lib/test.sh"
 
-run "$bp -I $in -O $tmp.1"
-assert_no_diff $tmp.1 $out.1
-rm $tmp.1
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+rm $tmp

diff --git a/bp_test/test/test_read_fasta b/bp_test/test/test_read_fasta
index 88f9018adc6f77716c3f6b0c3bbc502601340d8a..cc459f89673e9cc11284834f1c2f9d3c3b9fb63c 100755 (executable)
--- a/bp_test/test/test_read_fasta
+++ b/bp_test/test/test_read_fasta
@@ -2,10 +2,10 @@
 
 source "$BP_DIR/bp_test/lib/test.sh"
 
-run "$bp -i $in -O $tmp.1"
-assert_no_diff $tmp.1 $out.1
-rm $tmp.1
+run "$bp -i $in -O $tmp"
+assert_no_diff $tmp $out.1
+rm $tmp
 
-run "$bp -i $in -n 1 -O $tmp.2"
-assert_no_diff $tmp.2 $out.2
-rm $tmp.2
+run "$bp -i $in -n 1 -O $tmp"
+assert_no_diff $tmp $out.2
+rm $tmp

diff --git a/bp_test/test/test_read_tab b/bp_test/test/test_read_tab
index f1c73c8a5260b399445d3227d340e8e1982fa396..ed2da1a7d4cd3b15bb7a14b51352d6f95c356085 100755 (executable)
--- a/bp_test/test/test_read_tab
+++ b/bp_test/test/test_read_tab
@@ -2,34 +2,34 @@
 
 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 -O $tmp"
+assert_no_diff $tmp $out.1
+rm $tmp
 
-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 -O $tmp"
+assert_no_diff $tmp $out.2
+rm $tmp
 
-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 -k ORGANISM,SEQ,COUNT -O $tmp"
+assert_no_diff $tmp $out.3
+rm $tmp
 
-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 -O $tmp"
+assert_no_diff $tmp $out.4
+rm $tmp
 
-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.1 -s 1 -c 2,1 -k COUNT,SEQ -O $tmp"
+assert_no_diff $tmp $out.5
+rm $tmp
 
-run "$bp -i $in.2 -O $tmp.6"
-assert_no_diff $tmp.6 $out.6
-rm $tmp.6
+run "$bp -i $in.2 -O $tmp"
+assert_no_diff $tmp $out.6
+rm $tmp
 
-run "$bp -i $in.2 -n 1 -O $tmp.7"
-assert_no_diff $tmp.7 $out.7
-rm $tmp.7
+run "$bp -i $in.2 -n 1 -O $tmp"
+assert_no_diff $tmp $out.7
+rm $tmp
 
-run "$bp -i $in.3 -d ';' -O $tmp.8"
-assert_no_diff $tmp.8 $out.8
-rm $tmp.8
+run "$bp -i $in.3 -d ';' -O $tmp"
+assert_no_diff $tmp $out.8
+rm $tmp

diff --git a/bp_test/test/test_uppercase_seq b/bp_test/test/test_uppercase_seq
index 3f4ad21f730ced60ba7a07bbdaf6f852f9c00b5b..4266db8615e96094938fc886e5d4902d3ef70b56 100755 (executable)
--- a/bp_test/test/test_uppercase_seq
+++ b/bp_test/test/test_uppercase_seq
@@ -2,6 +2,6 @@
 
 source "$BP_DIR/bp_test/lib/test.sh"
 
-run "$bp -I $in -O $tmp.1"
-assert_no_diff $tmp.1 $out.1
-rm $tmp.1
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+rm $tmp

diff --git a/bp_test/test/test_write_fasta b/bp_test/test/test_write_fasta
index a2f5b0769e6e7d921291c4cdf70582fee397c883..9ae850296354a336707fc50f813b1e743a7bfb99 100755 (executable)
--- a/bp_test/test/test_write_fasta
+++ b/bp_test/test/test_write_fasta
@@ -2,10 +2,15 @@
 
 source "$BP_DIR/bp_test/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 -o $tmp -x"
+assert_no_diff $tmp $out.1
+rm $tmp
 
-run "write_fasta -I $in -w 4 -o $tmp.2 -x"
-assert_no_diff $tmp.2 $out.2
-rm $tmp.2
+run "write_fasta -I $in -w 4 -o $tmp -x"
+assert_no_diff $tmp $out.2
+rm $tmp
+
+# This one will not work for some reason?
+# run "write_fasta -I $in -w 4 -Z -o $tmp -x"
+# assert_no_diff $tmp $out.3
+# rm $tmp