src/hg/blastToPsl/tests/makefile 1.25
1.25 2010/04/16 17:32:12 markd
add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range
Index: src/hg/blastToPsl/tests/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/blastToPsl/tests/makefile,v
retrieving revision 1.24
retrieving revision 1.25
diff -b -B -U 4 -r1.24 -r1.25
--- src/hg/blastToPsl/tests/makefile 8 Feb 2010 03:14:55 -0000 1.24
+++ src/hg/blastToPsl/tests/makefile 16 Apr 2010 17:32:12 -0000 1.25
@@ -17,31 +17,8 @@
blockBugTest identityBugTest protMrnaEval1Test protMrnaEval2Test \
longDbNameTest multiLineDescTest tblastxTest tblastnTest \
blastpPsiTest psiNoHitsTest psiBadFormatTest blastpPsiWrapTest
-###
-# blastXmlToPsl
-###
-testBlastXmlToPsl: mrna1Test prot1Test prot2Test
-
-mrna1Test: mkdirs
- ${blastXmlToPsl} -scores=output/$@.bscores input/mrna1.blastn.xml output/$@.psl
- pslCheck -verbose=0 output/$@.psl
- diff -u expected/$@.psl output/$@.psl
- diff -u expected/$@.bscores output/$@.bscores
-
-prot1Test: mkdirs
- ${blastXmlToPsl} -scores=output/$@.bscores input/prot1.tblastn.xml output/$@.psl
- pslCheck -verbose=0 output/$@.psl
- diff -u expected/$@.psl output/$@.psl
- diff -u expected/$@.bscores output/$@.bscores
-
-prot2Test: mkdirs
- ${blastXmlToPsl} -scores=output/$@.bscores input/prot2.psiblast.xml output/$@.psl
- pslCheck -verbose=0 output/$@.psl
- diff -u expected/$@.psl output/$@.psl
- diff -u expected/$@.bscores output/$@.bscores
-
protMrnaTest: mkdirs
${blastToPsl} -scores=output/$@.bscores input/kgProtMRna1.blast output/$@.psl
pslCheck -verbose=0 output/$@.psl
diff -u expected/$@.psl output/$@.psl
@@ -159,8 +136,37 @@
diff -u expected/$@.psl output/$@.psl
diff -u expected/$@.bscores output/$@.bscores
diff -u expected/$@.err output/$@.err
+###
+# blastXmlToPsl
+###
+testBlastXmlToPsl: mrna1Test prot1Test prot2Test prot1NucCoordTest
+
+mrna1Test: mkdirs
+ ${blastXmlToPsl} -scores=output/$@.bscores input/mrna1.blastn.xml output/$@.psl
+ pslCheck -verbose=0 output/$@.psl
+ diff -u expected/$@.psl output/$@.psl
+ diff -u expected/$@.bscores output/$@.bscores
+
+prot1Test: mkdirs
+ ${blastXmlToPsl} -scores=output/$@.bscores input/prot1.tblastn.xml output/$@.psl
+ pslCheck -verbose=0 output/$@.psl
+ diff -u expected/$@.psl output/$@.psl
+ diff -u expected/$@.bscores output/$@.bscores
+
+prot2Test: mkdirs
+ ${blastXmlToPsl} -scores=output/$@.bscores input/prot2.psiblast.xml output/$@.psl
+ pslCheck -verbose=0 output/$@.psl
+ diff -u expected/$@.psl output/$@.psl
+ diff -u expected/$@.bscores output/$@.bscores
+
+prot1NucCoordTest: mkdirs
+ ${blastXmlToPsl} -convertToNucCoords input/prot1.tblastn.xml output/$@.psl
+ pslCheck -verbose=0 output/$@.psl
+ diff -u expected/$@.psl output/$@.psl
+
+
clean::
rm -rf output
mkdirs: