Commit d4460962 authored by Liubov Chuprikova's avatar Liubov Chuprikova
Browse files

Autopkgtest: continue to improve tests by checking its output content

parent 6576aed1

debian/copyright

+2 −1
Original line number Diff line number Diff line
@@ -14,13 +14,14 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr> 
License: public_domain



Files: debian/tests/test-data/nc0225.aso.gz

       debian/tests/test-data/dsRNA_viruses.ags.gz

       debian/tests/test-data/dsRNA_viruses.*

Copyright: 1996-2018 NCBI 

License: public_domain

Comment: 

 To dowload the files use:

    wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0225.aso.gz

    wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz

    wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Viruses/dsRNA_viruses.gene_info.gz



Files: debian/tests/test-data/trnascan-se_sample.output

Comment:

debian/source/include-binaries

+1 −0
Original line number Diff line number Diff line 
debian/tests/test-data/nc0225.aso.gz

debian/tests/test-data/dsRNA_viruses.ags.gz

debian/tests/test-data/dsRNA_viruses.gene_info.gz

debian/tests/run-unit-test

+71 −26
Original line number Diff line number Diff line
@@ -58,16 +58,83 @@ echo '---asn2gb test---' 
gbk="$(grep -c "^LOCUS " nc0225.gbk)"

[ $genes -eq $gbk ]



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

echo '---asn2xml test---'

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

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

[ -s nc0225.xml ]

dna_xml="$(grep -c '<Seq-inst_mol value="dna"/>' nc0225.xml)"

rna_xml="$(grep -c '<Seq-inst_mol value="rna"/>' nc0225.xml)"

proteins_xml="$(grep -c '<Seq-inst_mol value="aa"/>' nc0225.xml)"

[ $genes -eq $(expr $dna_xml + $rna_xml) ]

[ $proteins -eq $proteins_xml ]



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

echo '---cleanasn test---'

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

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

[ -s nc0225_cleaned.text ]

titles="$(grep -c " title \"" nc0225.text)"

titles_to_clean="$(grep -A 1 " descr {$" nc0225.text | grep -c " title \"")"

titles_left="$(grep -c " title \"" nc0225_cleaned.text)"

[ $(expr $titles - $titles_to_clean) -eq $titles_left ]



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

echo '---gene2xml test---'

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

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

[ -s dsRNA_viruses.xgs ]

# The content in dsRNA_viruses.gene_info mirrors the content in dsRNA_viruses.ags

first_id="$(awk 'NR==2{print $1}' dsRNA_viruses.gene_info)"

last_id="$(awk 'END{print $1}' dsRNA_viruses.gene_info)"

# check the beginning of the output

start_in="$(grep -c "^${first_id}" dsRNA_viruses.gene_info)"

start_out="$(grep -c "<Object-id_id>${first_id}</Object-id_id>" dsRNA_viruses.xgs)"

[ $start_in -eq $start_out ]

#check the ending of the output

end_in="$(grep -c "^${last_id}" dsRNA_viruses.gene_info)"

end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)"

[ $end_in -eq $end_out ]





# _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

check_GI()

{

	while read GI; do

		grep -q $GI $1

	done < $2

}

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

echo '---insdseqget test---'

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

/usr/bin/insdseqget -i GIs.txt > insdset.xml

[ -s insdset.xml ]

check_GI insdset.xml GIs.txt

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

echo '---idfetch test---'

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

/usr/bin/idfetch -G GIs.txt -o idfetch.text

[ -s idfetch.text ]

check_GI idfetch.text GIs.txt





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

echo '---vecscreen test---'

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

/usr/bin/vecscreen -f 3 < nc0225.fna > vecscreen.output

[ -s vecscreen.output ]

last_in="$(grep ">" nc0225.fna | tail -1 | sed 's/>//' | sed 's/ .*//')"

last_out="$(grep ">" vecscreen.output | tail -1 | sed 's/>Vector //' | sed 's/ .*//')"

[ $last_in==$last_out ]





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 ]
@@ -84,28 +151,10 @@ 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 ]
@@ -117,7 +166,3 @@ 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 ]

debian/tests/test-data/dsRNA_viruses.gene_info.gz

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debian/tests/test-data/trnascan-se_sample.output

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tRNAscan-SE v.2.0 (December 2017) - scan sequences for transfer RNAs

Copyright (C) 2017 Patricia Chan and Todd Lowe

                   University of California Santa Cruz
@@ -7,7 +6,7 @@ Freely distributed under the GNU General Public License (GPLv3) 
------------------------------------------------------------

Sequence file(s) to search:        /usr/share/doc/trnascan-se/examples/Example1.fa

Search Mode:                       Eukaryotic

Results written to:                testrun.out

Results written to:                trnascan-se_sample.output

Output format:                     Tabular

Searching with:                    Infernal First Pass->Infernal

Isotype-specific model scan:       Yes