src/hg/blastToPsl/tests/makefile 1.25

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 1000000 -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
@@ -1,167 +1,173 @@
 include ../../../inc/common.mk
 
 #blastToPsl = valgrind --tool=memcheck ../blastToPsl
 blastToPsl = blastToPsl
 
 #blastXmlToPsl = valgrind --tool=memcheck ../blastToPsl
 blastXmlToPsl = blastXmlToPsl
 
 all:
 
 test: testBlastToPsl testBlastXmlToPsl
 
 ###
 # blastToPsl
 ###
 testBlastToPsl:	protMrnaTest protDnaTest mrnaDnaTest mrnaDnaxTest \
 	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
 	diff -u expected/$@.bscores output/$@.bscores
 
 protDnaTest: mkdirs
 	${blastToPsl} -scores=output/$@.bscores input/kgProtDna1.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 mrnaDnaTest: mkdirs
 	${blastToPsl} input/mrnaDna1.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 mrnaDnaxTest: mkdirs
 	${blastToPsl} -pslx input/mrnaDna1.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # test case that cause huge target block start.
 blockBugTest: mkdirs
 	${blastToPsl} input/blockBug.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # handle id
 identityBugTest: mkdirs
 	${blastToPsl} input/identityBug.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # test E-value threshold filter
 protMrnaEval1Test: mkdirs
 	${blastToPsl} -eVal=1 -scores=output/$@.bscores input/kgProtMRna1.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 protMrnaEval2Test: mkdirs
 	${blastToPsl} -eVal=1e-10 -scores=output/$@.bscores input/kgProtMRna1.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 longDbNameTest: mkdirs
 	${blastToPsl} input/longDbName.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # multiline description broke parser
 multiLineDescTest: mkdirs
 	${blastToPsl} input/multiLineDesc.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # tblastx
 tblastxTest: mkdirs
 	${blastToPsl} -scores=output/$@.bscores input/tblastx.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 # tblastn
 tblastnTest: mkdirs
 	${blastToPsl} -scores=output/$@.bscores input/tblastn.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 
 # this test is currently disabled.  This file has Database: before Query= and
 # there are multiple queries for each Database:
 tblastnDbFirstTest: mkdirs
 	${blastToPsl} input/tblastnDbFirst.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 
 # this test is currently disabled, mega-blast is painful because
 # Database: comes before Query= and there are multiple queries for each
 # Database:.
 megaBlastTest: mkdirs
 	${blastToPsl} input/970.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # PSI-BLASTP 
 blastpPsiTest: mkdirs
 	${blastToPsl} -scores=output/$@.bscores input/blastpPsi.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 # PSI-BLASTP with Identities line wrapping
 blastpPsiWrapTest: mkdirs
 	${blastToPsl} -scores=output/$@.bscores input/blastpPsiWrap.blast output/$@.psl
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 # PSI-BLASTP with no hits
 psiNoHitsTest: mkdirs
 	${blastToPsl} -scores=output/$@.bscores input/psiNoHits.blast output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 	diff -u expected/$@.bscores output/$@.bscores
 
 # PSI-BLASTP produces bogus blocks where query starts at 0 and there is not
 # ending number on the line. Sbjct may be empty or have sequence.  These 
 # are ignored
 psiBadFormatTest: mkdirs
 	${blastToPsl} -scores=output/$@.bscores input/psiBadFormat.blast output/$@.psl >output/$@.err 2>&1
 	pslCheck -verbose=0 output/$@.psl
 	diff -u expected/$@.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:
 	@${MKDIR} output