8cbd73320598db4c37c75666e518622f82fbc326 markd Sun Jun 6 20:53:15 2021 -0700 added option for chromToUcsc to skip unmapped chromosomes rather than error diff --git src/utils/chromToUcsc/tests/makefile src/utils/chromToUcsc/tests/makefile index 9c21ead..9973976 100644 --- src/utils/chromToUcsc/tests/makefile +++ src/utils/chromToUcsc/tests/makefile @@ -1,26 +1,34 @@ kentSrc = ../../.. include ../../../inc/common.mk all: mkdir -p out # alas, our automated tests cannot output anything to stderr, as otherwise emails will be sent - python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a hg19.chromAlias.tsv 2> /dev/null - python2 ${DESTBINDIR}/chromToUcsc -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2> /dev/null + rm -f out/test.err + python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a hg19.chromAlias.tsv 2>> out/test.err + python2 ${DESTBINDIR}/chromToUcsc -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2>> out/test.err diff out/hg19.bed expected/hg19.bed diff out/mm10.bed expected/mm10.bed - python3 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a hg19.chromAlias.tsv 2> /dev/null - python3 ${DESTBINDIR}/chromToUcsc -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2> /dev/null + python3 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a hg19.chromAlias.tsv 2>> out/test.err + python3 ${DESTBINDIR}/chromToUcsc -i in/mm10.bed -o out/mm10.bed -a mm10.chromAlias.tsv 2>> out/test.err diff out/hg19.bed expected/hg19.bed diff out/mm10.bed expected/mm10.bed - python3 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromAlias.txt.gz 2> /dev/null + python3 ${DESTBINDIR}/chromToUcsc -i in/hg19.bed -o out/hg19.bed -a https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromAlias.txt.gz 2>> out/test.err diff out/hg19.bed expected/hg19.bed - python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.vcf.gz -o out/hg19.vcf -a hg19.chromAlias.tsv 2> /dev/null + python2 ${DESTBINDIR}/chromToUcsc -i in/hg19.vcf.gz -o out/hg19.vcf -a hg19.chromAlias.tsv 2>> out/test.err diff out/hg19.vcf expected/hg19.vcf - python3 ${DESTBINDIR}/chromToUcsc -i in/mm10.ebi.sam.gz -a mm10.chromAlias.tsv -o out/mm10.ebi.sam 2> /dev/null + python3 ${DESTBINDIR}/chromToUcsc -i in/mm10.ebi.sam.gz -a mm10.chromAlias.tsv -o out/mm10.ebi.sam 2>> out/test.err diff out/mm10.ebi.sam expected/mm10.ebi.sam - python3 ${DESTBINDIR}/chromToUcsc -i in/grc38.100.gtf.gz -a mm10.chromAlias.tsv -o out/mm10.gtf 2> /dev/null + python3 ${DESTBINDIR}/chromToUcsc -i in/grc38.100.gtf.gz -a mm10.chromAlias.tsv -o out/mm10.gtf 2>> out/test.err diff out/mm10.gtf expected/mm10.gtf + python3 ${DESTBINDIR}/chromToUcsc -i in/grc38.100.gtf.gz -a mm10.chromAlias.tsv -o out/mm10.gtf 2>> out/test.err + diff out/mm10.gtf expected/mm10.gtf + python3 /cluster/home/markd/kent/bin/x86_64/chromToUcsc -s -i in/mm10.bad-names.bed -a mm10.chromAlias.tsv -o out/mm10.bad-names.bed >& out/mm10.bad-names.err + diff expected/mm10.bad-names.err out/mm10.bad-names.err + diff expected/mm10.bad-names.bed out/mm10.bad-names.bed + +test: all clean: rm -f out/*