c6753d13e623ebd80e64ebff2296f7d596695442 markd Wed Jul 10 19:46:37 2019 -0700 added test case for transcipt-only annotations diff --git src/hg/utils/gff3ToGenePred/tests/makefile src/hg/utils/gff3ToGenePred/tests/makefile index 09788a6..30b9b15 100644 --- src/hg/utils/gff3ToGenePred/tests/makefile +++ src/hg/utils/gff3ToGenePred/tests/makefile @@ -1,29 +1,30 @@ kentSrc = ../../../.. include ../../../../inc/common.mk gff3ToGenePred = ${DESTBINDIR}/gff3ToGenePred # sh commands to deal with gff3ToGenePred shouldhave failed and didn't cmdShouldFail = echo "Error: command should have failed" >&2; false all:: test:: geneMRnaTest noGeneMRnaTest geneMRnaHonorTest discontinuousTest multCdsOutOfExonTest \ noIdTest errCases1Test bogusQuotesTest noExonsTest geneTranscriptTest transcriptCdsParentTest \ minimalGenesTest geneDefaultStatusUnknownTest useNameTest nameAttrIdTest nameAttrNameTest \ - frameShiftTest mm10GencodeTest ncbiSegmentsTest ncbiProblemsTest makeBadTest + frameShiftTest mm10GencodeTest ncbiSegmentsTest ncbiProblemsTest makeBadTest \ + transcriptOnlyTest geneMRnaTest: mkout ${gff3ToGenePred} input/geneMRna.gff3 output/$@.gp diff expected/$@.gp output/$@.gp noGeneMRnaTest: mkout ${gff3ToGenePred} input/noGeneMRna.gff3 output/$@.gp diff expected/$@.gp output/$@.gp geneMRnaHonorTest: mkout ${gff3ToGenePred} -honorStartStopCodons input/geneMRna.gff3 output/$@.gp diff expected/$@.gp output/$@.gp geneDefaultStatusUnknownTest: mkout ${gff3ToGenePred} -defaultCdsStatusToUnknown input/geneMRna.gff3 output/$@.gp @@ -108,20 +109,26 @@ # various NCBI problem cases ncbiProblemsTest: mkout ${gff3ToGenePred} -warnAndContinue -geneNameAttr=gene -refseqHacks -attrsOut=output/$@.attrs input/ncbiProblems.gff3 output/$@.gp > output/$@.out 2>&1 diff expected/$@.gp output/$@.gp diff expected/$@.attrs output/$@.attrs diff expected/$@.out output/$@.out # -warnAndContinue on maker file with missing gene/mrna records. This test this option on # GFF3 parse tests, not just genePred conversion makeBadTest: mkout ${gff3ToGenePred} -warnAndContinue -attrsOut=output/$@.attrs input/makerBad.gff3 output/$@.gp > output/$@.out 2>&1 diff expected/$@.gp output/$@.gp diff expected/$@.attrs output/$@.attrs diff expected/$@.out output/$@.out +# pseudogene annotations as transcripts-only. Yet another non-standard variation +transcriptOnlyTest: mkout + ${gff3ToGenePred} -allowMinimalGenes input/transcriptOnly.gff3 output/$@.gp + diff expected/$@.gp output/$@.gp + + mkout: @mkdir -p output clean:: rm -rf output