[med-svn] [Git][med-team/ncbi-tools6][master] Autopkgtest. More tests
Liubov Chuprikova
gitlab at salsa.debian.org
Thu Mar 29 14:15:44 UTC 2018
Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6
Commits:
3bf17382 by Liubov Chuprikova at 2018-03-29T13:55:29+00:00
Autopkgtest. More tests
- - - - -
5 changed files:
- debian/changelog
- debian/copyright
- debian/ncbi-tools-bin.docs
- debian/tests/run-unit-test
- + debian/tests/test-data/trnascan-se_sample.output
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -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 ]
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -13,13 +13,19 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer at pasteur.fr>
2001-2017 Aaron M. Ucko <ucko at 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
+ 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:
=====================================
debian/ncbi-tools-bin.docs
=====================================
--- a/debian/ncbi-tools-bin.docs
+++ b/debian/ncbi-tools-bin.docs
@@ -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
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -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
@@ -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 ]
@@ -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
=====================================
--- /dev/null
+++ b/debian/tests/test-data/trnascan-se_sample.output
@@ -0,0 +1,50 @@
+
+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
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111
---
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/3bf173820570f09fad0d307020082755a813d111
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