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#!/bin/bash
set -e
pkg="ncbi-tools-bin"
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/test-data/* .
cp /usr/share/doc/${pkg}/{asnpub.all.gz,medline.ent} .
cp /usr/share/ncbi/data/autofix.prt .
cp /usr/share/ncbi/data/UniVec.* .
gunzip *.gz
##################################################################
echo '---asn2asn test---'
##################################################################
/usr/bin/asn2asn -i nc0225.aso -b -o nc0225.text
/usr/bin/asn2asn -i nc0225.text -s -o nc0225_new.aso
[ -s nc0225.text ]
[ -s nc0225_new.aso ]
diff nc0225.aso nc0225_new.aso
rm nc0225.aso nc0225_new.aso
##################################################################
echo '---asn2all test---'
##################################################################
/usr/bin/asn2all -i nc0225.text -f g -o nc0225.nuc -v nc0225.prt
[ -s nc0225.nuc ]
genes_dna="$(grep -c " mol dna ," nc0225.text)"
genes_rna="$(grep -c " mol rna ," nc0225.text)"
genes=$(expr $genes_dna + $genes_rna)
nuc="$(grep -c "^LOCUS " nc0225.nuc)"
[ $genes -eq $nuc ]
[ -s nc0225.prt ]
proteins="$(grep -c " mol aa ," nc0225.text)"
prt="$(grep -c "^LOCUS " nc0225.prt)"
[ $proteins -eq $prt ]
##################################################################
echo '---asn2fsa test---'
##################################################################
/usr/bin/asn2fsa -i nc0225.text -a t -o nc0225.fna -v nc0225.faa
[ -s nc0225.fna ]
fna="$(grep -c "^>" nc0225.fna)"
[ $genes -eq $fna ]
[ -s nc0225.faa ]
faa="$(grep -c "^>" nc0225.faa)"
[ $proteins -eq $faa ]
##################################################################
echo '---asn2gb test---'
##################################################################
/usr/bin/asn2gb -i nc0225.text -a t -o nc0225.gbk
[ -s nc0225.gbk ]
gbk="$(grep -c "^LOCUS " nc0225.gbk)"
[ $genes -eq $gbk ]
echo '---asn2idx test---'
/usr/bin/asn2idx -p . -x .text < nc0225.text
[ -s nc0225.idx ]
[ -s master.idx ]
echo '---asn2xml test---'
/usr/bin/asn2xml -i nc0225.text -b F -o nc0225.xml
[ -s nc0225.xml ]
echo '---asndisc test---'
/usr/bin/asndisc -i nc0225.text -a t -o nc0225.disc
[ -s nc0225.disc ]
echo '---asnval test---'
/usr/bin/asnval -i nc0225.text -a t -o nc0225.val -Q 2
[ -s nc0225.val ]
echo '---asnmacro test---'
/usr/bin/asnmacro -i nc0225.text -m autofix.prt -o asnmacro.output
[ -s asnmacro.output ]
echo '---asntool test---'
/usr/bin/asntool -m asnpub.all -v medline.ent -p asntool.output
[ -s asntool.output ]
echo '---cleanasn test---'
/usr/bin/cleanasn -a t -D t -i nc0225.text -o nc0225_cleaned.text
[ -s nc0225_cleaned.text ]
echo '---debruijn test---'
/usr/bin/debruijn -a ncbistdaa -n 4 > debruijn.output
[ -s debruijn.output ]
echo '---gene2xml test---'
/usr/bin/gene2xml -b -i dsRNA_viruses.ags -o dsRNA_viruses.xgs
[ -s dsRNA_viruses.xgs ]
# _insdseqget_ and _idfetch_ testing requires internet connection.
# Comment the lines below to skip the testing.
grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
echo '---insdseqget test---'
/usr/bin/insdseqget -n -i GIs.txt > insdset.xml
[ -s insdset.xml ]
echo '---idfetch test---'
/usr/bin/idfetch -G GIs.txt -t 2 -o idfetch.aso
[ -s idfetch.aso ]
echo '---tbl2asn test---'
/usr/bin/tbl2asn -t Sc_16.sbt -i Sc_16.fsa
[ -s Sc_16.sqn ]
echo '---trna2sap test---'
/usr/bin/trna2sap < trnascan-se_sample.output > trna2sap.output
[ -s trna2sap.output ]
echo '---trna2tbl test---'
/usr/bin/trna2tbl < trnascan-se_sample.output > trna2tbl.output
[ -s trna2tbl.output ]
echo '---vecscreen test---'
/usr/bin/vecscreen -f 3 < nc0225.fna > vecscreen.output
[ -s vecscreen.output ]
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