Autopkgtest: improved a couple of tests by checking its output content

cp /usr/share/ncbi/data/UniVec.* .

gunzip *.gz

echo '---asn2all test---'

/usr/bin/asn2all -i nc0225.aso -b -f g -o nc0225.nuc -v nc0225.prt

[ -s nc0225.nuc ]

[ -s nc0225.prt ]

##################################################################

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.aso -b -a t -o nc0225.fna -v nc0225.faa

##################################################################

/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.aso -b -a t -o nc0225.gbk

##################################################################

/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 -b -p . < nc0225.aso

/usr/bin/asn2idx -p . -x .text < nc0225.text

[ -s nc0225.idx ]

[ -s master.idx ]

echo '---asn2xml test---'

/usr/bin/asn2xml -i nc0225.aso -o nc0225.xml

/usr/bin/asn2xml -i nc0225.text -b F -o nc0225.xml

[ -s nc0225.xml ]

echo '---asndisc test---'

/usr/bin/asndisc -i nc0225.aso -b -a t -o nc0225.disc

/usr/bin/asndisc -i nc0225.text -a t -o nc0225.disc

[ -s nc0225.disc ]

echo '---asnval test---'

/usr/bin/asnval -i nc0225.aso -b -a t -o nc0225.val

[ -f nc0225.val ]

[ ! -s nc0225.val ] # empty

/usr/bin/asnval -i nc0225.text -a t -o nc0225.val -Q 2

[ -s nc0225.val ]

echo '---asnmacro test---'

/usr/bin/asnmacro -i nc0225.aso -b -m autofix.prt -o asnmacro.output

/usr/bin/asnmacro -i nc0225.text -m autofix.prt -o asnmacro.output

[ -s asnmacro.output ]

echo '---asntool test---'

[ -s asntool.output ]

echo '---cleanasn test---'

/usr/bin/cleanasn -b -a t -D t -i nc0225.aso -o nc0225_cleaned.aso

[ -s nc0225_cleaned.aso ]

/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

/usr/bin/gene2xml -b -i dsRNA_viruses.ags -o dsRNA_viruses.xgs

[ -s dsRNA_viruses.xgs ]

grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt

# _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 ]