195a08fae15bd2ca55f2f2ed11d0c359521efcc4
markd
  Wed May 17 09:13:21 2023 -0700
added program to convert protein/protein or protein NA PSLs to NA/NA PSLs.  The multiplies coordinates by three; trimming any overlapping blocks that might be creates.  This is intended to use with pslMap

diff --git src/utils/pslProtToRnaCoords/tests/makefile src/utils/pslProtToRnaCoords/tests/makefile
new file mode 100644
index 0000000..6ae9239
--- /dev/null
+++ src/utils/pslProtToRnaCoords/tests/makefile
@@ -0,0 +1,42 @@
+
+kentSrc = ../../..
+include ${kentSrc}/inc/common.mk
+
+pslProtToRnaCoords = ${DESTBINDIR}/pslProtToRnaCoords
+blastToPsl = ${DESTBINDIR}/blastToPsl
+pslCheck = ${DESTBINDIR}/pslCheck
+
+pslMapTestIn = ../../pslMap/tests/input
+
+all:
+
+test: kgProtTest spAnnotTest spIsoCanonTest spGencodeTest
+
+kgProtTest: mkdirs
+	${blastToPsl} ${pslMapTestIn}/kgProtMRna.blast output/kgProtMRna.psl
+	${pslProtToRnaCoords} output/kgProtMRna.psl output/$@.psl
+	${pslCheck} -verbose=0 output/$@.psl
+	diff -u expected/$@.psl output/$@.psl
+
+spAnnotTest: mkdirs
+	${pslProtToRnaCoords} input/swissprotAnnotsToProt.psl output/$@.psl
+	${pslCheck} -verbose=0  output/$@.psl
+	diff -u expected/$@.psl output/$@.psl
+
+spIsoCanonTest: mkdirs
+	${pslProtToRnaCoords} input/swissprotIsoCanon.psl output/$@.psl
+	${pslCheck} -verbose=0 output/$@.psl
+	diff -u expected/$@.psl output/$@.psl
+
+# this tests fixing overlapping blocks
+spGencodeTest: mkdirs
+	${pslProtToRnaCoords} input/swissprotGencode.psl output/$@.psl
+	${pslCheck} -verbose=0 output/$@.psl
+	diff -u expected/$@.psl output/$@.psl
+
+clean::
+	rm -rf output
+
+mkdirs:
+	@${MKDIR} output
+