Loading debian/changelog +1 −1 Original line number Diff line number Diff line Loading @@ -2,7 +2,7 @@ ncbi-tools6 (6.1.20170106-3) UNRELEASED; urgency=medium [ Liubov Chuprikova ] * Team upload. * Added autopkgtest for part of ncbi-tools-bin. * Added autopkgtest for ncbi-tools-bin. Closes: #879619 [ Aaron M. Ucko ] Loading debian/copyright +10 −4 Original line number Diff line number Diff line Loading @@ -13,14 +13,20 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr> 2001-2017 Aaron M. Ucko <ucko@debian.org> License: public_domain Files: debian/tests/test-data Files: debian/tests/test-data/nc0305.aso.gz debian/tests/test-data/dsRNA_viruses.ags.gz Copyright: 1996-2018 NCBI License: public_domain Comment: GenBank Release 224.0 Comment: To dowload the files use: wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz Files: debian/tests/test-data/trnascan-se_sample.output Comment: The file was generated by tRNAscan-SE 2.0: tRNAscan-SE -d -y -o trnascan-se_sample.output /usr/share/doc/trnascan-se/examples/Example1.fa License: public_domain The NCBI toolkit has been put into the public domain, completely unfettered: . Loading debian/ncbi-tools-bin.docs +2 −0 Original line number Diff line number Diff line Loading @@ -4,3 +4,5 @@ doc/tbl2asn.txt debian/README.test debian/tests/run-unit-test debian/tests/test-data asn/asnpub.all demo/medline.ent debian/tests/run-unit-test +17 −6 Original line number Diff line number Diff line Loading @@ -7,11 +7,9 @@ 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/* . gunzip * gunzip nc0305.aso.gz echo '---asn2all test---' /usr/bin/asn2all -i nc0305.aso -b -f g -o nc0305.nuc -v nc0305.prt Loading Loading @@ -58,12 +56,12 @@ echo '---debruijn test---' [ -s debruijn.output ] echo '---gene2xml test---' /usr/bin/gene2xml -b -i dsRNA_viruses.ags -o dsRNA_viruses.xgs /usr/bin/gene2xml -c -b -i dsRNA_viruses.ags.gz -o dsRNA_viruses.xgs [ -s dsRNA_viruses.xgs ] grep 'GI:' nc0305.gbk | head | sed 's/.*GI://' > GIs.txt # insdseqget and idfetch testing requires internet connection. Comment lines below # to skip the testing. # _insdseqget_ and _idfetch_ testing requires internet connection. # Comment the lines below to skip the testing. echo '---insdseqget test---' /usr/bin/insdseqget -n -i GIs.txt > insdset.xml [ -s insdset.xml ] Loading @@ -71,3 +69,16 @@ echo '---idfetch test---' /usr/bin/idfetch -G GIs.txt -t 2 -o idfetch.aso [ -s idfetch.aso ] 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 ] cp /usr/share/doc/${pkg}/{asnpub.all.gz,medline.ent} . gunzip asnpub.all.gz echo '---asntool test---' /usr/bin/asntool -m asnpub.all -v medline.ent -p asntool.output [ -s asntool.output ] debian/tests/test-data/trnascan-se_sample.output 0 → 100644 +50 −0 Original line number Diff line number Diff line 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 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 Output format: Tabular Searching with: Infernal First Pass->Infernal Isotype-specific model scan: Yes Covariance model: /usr/share/trnascan-se/models/TRNAinf-euk.cm /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm Infernal first pass cutoff score: 10 Temporary directory: /tmp ------------------------------------------------------------ Status: Phase I: Searching for tRNAs with HMM-enabled Infernal Status: Phase I: Searching for tRNAs with HMM-enabled Infernal Scanned seqs: 0 (at CELF22B7) /usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_Domain.out /usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_SeC.out 1 seqs scanned, 1 seqs had at least one hit. 5 total tRNAs predicted in first pass scans Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan Scanning CELF22B7 /usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_Domain.out /usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_SeC.out /usr/bin/cmsearch -g --toponly --notextw /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_trunc_cm_Domain.out /usr/bin/cmscan -g --mid --toponly --notrunc --fmt 2 --tblout /tmp/tscan26061_iso_cm.tab -o /tmp/tscan26061_iso_cm.out /usr/share/trnascan-se/models/TRNAinf-euk-iso /tmp/tscan26061.trna CELF22B7.tRNA1-LeuCAA: Infernal type= Leu Score= 74.2 CELF22B7.tRNA2-SerAGA: Infernal type= Ser Score= 81.6 CELF22B7.tRNA3-PheGAA: Infernal type= Phe Score= 82.5 CELF22B7.tRNA4-PheGAA: Infernal type= Phe Score= 82.5 CELF22B7.tRNA5-ProCGG: Infernal type= Pro Score= 71.5 End Time: Tue Mar 27 23:02:00 2018 Sequence tRNA Bounds tRNA Anti Intron Bounds Inf Hit Name tRNA # Begin End Type Codon Begin End Score Origin Note -------- ------ ----- ------ ---- ----- ----- ---- ------ ------ ------ CELF22B7 1 12619 12738 Leu CAA 12657 12692 74.2 Inf CELF22B7 2 19480 19561 Ser AGA 0 0 81.6 Inf CELF22B7 3 26367 26439 Phe GAA 0 0 82.5 Inf CELF22B7 4 26992 26920 Phe GAA 0 0 82.5 Inf CELF22B7 5 23765 23694 Pro CGG 0 0 71.5 Inf Loading
debian/changelog +1 −1 Original line number Diff line number Diff line Loading @@ -2,7 +2,7 @@ ncbi-tools6 (6.1.20170106-3) UNRELEASED; urgency=medium [ Liubov Chuprikova ] * Team upload. * Added autopkgtest for part of ncbi-tools-bin. * Added autopkgtest for ncbi-tools-bin. Closes: #879619 [ Aaron M. Ucko ] Loading
debian/copyright +10 −4 Original line number Diff line number Diff line Loading @@ -13,14 +13,20 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr> 2001-2017 Aaron M. Ucko <ucko@debian.org> License: public_domain Files: debian/tests/test-data Files: debian/tests/test-data/nc0305.aso.gz debian/tests/test-data/dsRNA_viruses.ags.gz Copyright: 1996-2018 NCBI License: public_domain Comment: GenBank Release 224.0 Comment: To dowload the files use: wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz Files: debian/tests/test-data/trnascan-se_sample.output Comment: The file was generated by tRNAscan-SE 2.0: tRNAscan-SE -d -y -o trnascan-se_sample.output /usr/share/doc/trnascan-se/examples/Example1.fa License: public_domain The NCBI toolkit has been put into the public domain, completely unfettered: . Loading
debian/ncbi-tools-bin.docs +2 −0 Original line number Diff line number Diff line Loading @@ -4,3 +4,5 @@ doc/tbl2asn.txt debian/README.test debian/tests/run-unit-test debian/tests/test-data asn/asnpub.all demo/medline.ent
debian/tests/run-unit-test +17 −6 Original line number Diff line number Diff line Loading @@ -7,11 +7,9 @@ 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/* . gunzip * gunzip nc0305.aso.gz echo '---asn2all test---' /usr/bin/asn2all -i nc0305.aso -b -f g -o nc0305.nuc -v nc0305.prt Loading Loading @@ -58,12 +56,12 @@ echo '---debruijn test---' [ -s debruijn.output ] echo '---gene2xml test---' /usr/bin/gene2xml -b -i dsRNA_viruses.ags -o dsRNA_viruses.xgs /usr/bin/gene2xml -c -b -i dsRNA_viruses.ags.gz -o dsRNA_viruses.xgs [ -s dsRNA_viruses.xgs ] grep 'GI:' nc0305.gbk | head | sed 's/.*GI://' > GIs.txt # insdseqget and idfetch testing requires internet connection. Comment lines below # to skip the testing. # _insdseqget_ and _idfetch_ testing requires internet connection. # Comment the lines below to skip the testing. echo '---insdseqget test---' /usr/bin/insdseqget -n -i GIs.txt > insdset.xml [ -s insdset.xml ] Loading @@ -71,3 +69,16 @@ echo '---idfetch test---' /usr/bin/idfetch -G GIs.txt -t 2 -o idfetch.aso [ -s idfetch.aso ] 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 ] cp /usr/share/doc/${pkg}/{asnpub.all.gz,medline.ent} . gunzip asnpub.all.gz echo '---asntool test---' /usr/bin/asntool -m asnpub.all -v medline.ent -p asntool.output [ -s asntool.output ]
debian/tests/test-data/trnascan-se_sample.output 0 → 100644 +50 −0 Original line number Diff line number Diff line 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 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 Output format: Tabular Searching with: Infernal First Pass->Infernal Isotype-specific model scan: Yes Covariance model: /usr/share/trnascan-se/models/TRNAinf-euk.cm /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm Infernal first pass cutoff score: 10 Temporary directory: /tmp ------------------------------------------------------------ Status: Phase I: Searching for tRNAs with HMM-enabled Infernal Status: Phase I: Searching for tRNAs with HMM-enabled Infernal Scanned seqs: 0 (at CELF22B7) /usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_Domain.out /usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_SeC.out 1 seqs scanned, 1 seqs had at least one hit. 5 total tRNAs predicted in first pass scans Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan Scanning CELF22B7 /usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_Domain.out /usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_SeC.out /usr/bin/cmsearch -g --toponly --notextw /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_trunc_cm_Domain.out /usr/bin/cmscan -g --mid --toponly --notrunc --fmt 2 --tblout /tmp/tscan26061_iso_cm.tab -o /tmp/tscan26061_iso_cm.out /usr/share/trnascan-se/models/TRNAinf-euk-iso /tmp/tscan26061.trna CELF22B7.tRNA1-LeuCAA: Infernal type= Leu Score= 74.2 CELF22B7.tRNA2-SerAGA: Infernal type= Ser Score= 81.6 CELF22B7.tRNA3-PheGAA: Infernal type= Phe Score= 82.5 CELF22B7.tRNA4-PheGAA: Infernal type= Phe Score= 82.5 CELF22B7.tRNA5-ProCGG: Infernal type= Pro Score= 71.5 End Time: Tue Mar 27 23:02:00 2018 Sequence tRNA Bounds tRNA Anti Intron Bounds Inf Hit Name tRNA # Begin End Type Codon Begin End Score Origin Note -------- ------ ----- ------ ---- ----- ----- ---- ------ ------ ------ CELF22B7 1 12619 12738 Leu CAA 12657 12692 74.2 Inf CELF22B7 2 19480 19561 Ser AGA 0 0 81.6 Inf CELF22B7 3 26367 26439 Phe GAA 0 0 82.5 Inf CELF22B7 4 26992 26920 Phe GAA 0 0 82.5 Inf CELF22B7 5 23765 23694 Pro CGG 0 0 71.5 Inf
