[med-svn] [Git][med-team/ncbi-tools6][master] Autopkgtest: tests for gbseqget and nps2gps
Liubov Chuprikova
gitlab at salsa.debian.org
Tue Apr 17 14:59:09 BST 2018
Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6
Commits:
09d2462c by Liubov Chuprikova at 2018-04-17T13:57:09+00:00
Autopkgtest: tests for gbseqget and nps2gps
- - - - -
2 changed files:
- debian/tests/run-unit-test
- + debian/tests/test-data/idfetch_g1234.npset
Changes:
=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -116,6 +116,12 @@ grep 'GI:' nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
if nc -z -w 1 www.ncbi.nlm.nih.gov 80; then
##################################################################
+ echo '---gbseqget test---'
+ ##################################################################
+ /usr/bin/gbseqget -i GIs.txt -o gbseqget.xml
+ [ -s gbseqget.xml ]
+ check_GI gbseqget.xml GIs.txt
+ ##################################################################
echo '---insdseqget test---'
##################################################################
/usr/bin/insdseqget -i GIs.txt > insdset.xml
@@ -127,13 +133,6 @@ if nc -z -w 1 www.ncbi.nlm.nih.gov 80; then
/usr/bin/idfetch -G GIs.txt -o idfetch.text
[ -s idfetch.text ]
check_GI idfetch.text GIs.txt
-
- ##################################################################
- echo '---makeset test---'
- ##################################################################
- echo 'idfetch.text' > files
- /usr/bin/makeset -i files -o makeset.aso
- [ -s makeset.aso ]
fi
@@ -183,6 +182,15 @@ echo '---gil2bin test---'
/usr/bin/gil2bin -i GIs.txt -o GIs.bin
[ -s GIs.bin ]
+echo '---makeset test---'
+echo 'idfetch_g1234.npset' > files
+/usr/bin/makeset -i files -o makeset.output
+[ -s makeset.output ]
+
+echo '---nps2gps test---'
+/usr/bin/nps2gps -i idfetch_g1234.npset -o nps2gps.output
+[ -s nps2gps.output ]
+
echo '---tbl2asn test---'
/usr/bin/tbl2asn -t Sc_16.sbt -i Sc_16.fsa
[ -s Sc_16.sqn ]
=====================================
debian/tests/test-data/idfetch_g1234.npset
=====================================
--- /dev/null
+++ b/debian/tests/test-data/idfetch_g1234.npset
@@ -0,0 +1,457 @@
+Seq-entry ::= set {
+ level 1 ,
+ class nuc-prot ,
+ descr {
+ source {
+ org {
+ taxname "Ovis aries" ,
+ common "sheep" ,
+ db {
+ {
+ db "taxon" ,
+ tag
+ id 9940 } } ,
+ orgname {
+ name
+ binomial {
+ genus "Ovis" ,
+ species "aries" } ,
+ mod {
+ {
+ subtype strain ,
+ subname "domestic" } } ,
+ lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
+ Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla;
+ Ruminantia; Pecora; Bovidae; Caprinae; Ovis" ,
+ gcode 1 ,
+ mgcode 2 ,
+ div "MAM" } } ,
+ subtype {
+ {
+ subtype other ,
+ name "Allele: C4-2H.1" } } } ,
+ pub {
+ pub {
+ sub {
+ authors {
+ names
+ std {
+ {
+ name
+ name {
+ last "Ren" ,
+ initials "X." } } } ,
+ affil
+ str "X. Ren, The MRC Immunochemistry Unit, Dept of Biochemistry,
+ University of Oxford, South Parks Road, Oxford OX1 3QU, UK" } ,
+ medium other ,
+ date
+ std {
+ year 1992 ,
+ month 6 ,
+ day 22 } } } } ,
+ pub {
+ pub {
+ pmid 8423050 ,
+ article {
+ title {
+ name "The thioester and isotypic sites of complement component C4
+ in sheep and cattle." } ,
+ authors {
+ names
+ std {
+ {
+ name
+ name {
+ last "Ren" ,
+ initials "X.D." } } ,
+ {
+ name
+ name {
+ last "Dodds" ,
+ initials "A.W." } } ,
+ {
+ name
+ name {
+ last "Law" ,
+ initials "S.K." } } } ,
+ affil
+ str "Department of Biochemistry, University of Oxford, UK." } ,
+ from
+ journal {
+ title {
+ iso-jta "Immunogenetics" ,
+ ml-jta "Immunogenetics" ,
+ issn "0093-7711" ,
+ name "Immunogenetics" } ,
+ imp {
+ date
+ std {
+ year 1993 } ,
+ volume "37" ,
+ issue "2" ,
+ pages "120-128" ,
+ language "eng" ,
+ pubstatus ppublish ,
+ history {
+ {
+ pubstatus pubmed ,
+ date
+ std {
+ year 1993 ,
+ month 1 ,
+ day 1 } } ,
+ {
+ pubstatus medline ,
+ date
+ std {
+ year 1993 ,
+ month 1 ,
+ day 1 ,
+ hour 0 ,
+ minute 1 } } ,
+ {
+ pubstatus other ,
+ date
+ std {
+ year 1993 ,
+ month 1 ,
+ day 1 ,
+ hour 0 ,
+ minute 0 } } } } } ,
+ ids {
+ doi "10.1007/BF00216835" ,
+ pubmed 8423050 } } } } ,
+ comment "See also X66994-99" ,
+ update-date
+ std {
+ year 2016 ,
+ month 7 ,
+ day 14 } } ,
+ seq-set {
+ seq {
+ id {
+ embl {
+ accession "X66994" ,
+ version 1 } ,
+ gi 1234 } ,
+ descr {
+ title "O.aries (C4-2H.1) C4 gene" ,
+ molinfo {
+ biomol genomic } ,
+ embl {
+ div mam ,
+ creation-date
+ std {
+ year 1992 ,
+ month 7 ,
+ day 10 } ,
+ update-date
+ std {
+ year 2006 ,
+ month 11 ,
+ day 14 } ,
+ keywords {
+ "complement component" ,
+ "complement component C4" } } ,
+ create-date
+ std {
+ year 1992 ,
+ month 7 ,
+ day 10 } } ,
+ inst {
+ repr raw ,
+ mol dna ,
+ length 945 ,
+ seq-data
+ ncbi2na '50A79AA040538577E9D411E9E7D59C5E8421624BA25E7955E214285996E
+8DD35202BDE2E49A624A2EA94A22A4BC3A09EA497ABAD224A8222392D54BA00AAF17FD45ECEBB8
+5D2793F5FD429C4668D4A0FD80088EBD73AA7EBC4DA84B245EB8BFA28BB5EAEEEA2A94AFEB8492
+25273CEA2240CA1592CFAD53B91ECBB7229CD509CE5FDDD7729D1A5FEE78231E2FE9528D2BA9A7
+71C009C4A21253BA79FD5241A8E3A74F51855ED7BCD44A8CE4ACE89EA29EA52A9128AA22D15E55
+D9476EBE79E79E70B6F12DBB5077B9855321A49514A759ED5EABDD4A42047A2EAF94FD7DD43939
+0BBFDE547D052A29F2EA098C0'H } ,
+ annot {
+ {
+ data
+ ftable {
+ {
+ data
+ rna {
+ type mRNA } ,
+ partial TRUE ,
+ location
+ mix {
+ int {
+ from 0 ,
+ to 133 ,
+ id
+ gi 1234 ,
+ fuzz-from
+ lim lt } ,
+ int {
+ from 298 ,
+ to 373 ,
+ id
+ gi 1234 } ,
+ int {
+ from 530 ,
+ to 686 ,
+ id
+ gi 1234 } ,
+ int {
+ from 924 ,
+ to 944 ,
+ id
+ gi 1234 ,
+ fuzz-to
+ lim gt } } } ,
+ {
+ data
+ imp {
+ key "exon" } ,
+ partial TRUE ,
+ location
+ int {
+ from 0 ,
+ to 133 ,
+ id
+ gi 1234 ,
+ fuzz-from
+ lim lt } ,
+ qual {
+ {
+ qual "number" ,
+ val "24" } } } ,
+ {
+ data
+ imp {
+ key "misc_feature" } ,
+ comment "thioester site" ,
+ location
+ int {
+ from 7 ,
+ to 18 ,
+ id
+ gi 1234 } } ,
+ {
+ data
+ imp {
+ key "intron" } ,
+ location
+ int {
+ from 134 ,
+ to 297 ,
+ id
+ gi 1234 } ,
+ qual {
+ {
+ qual "number" ,
+ val "24" } } } ,
+ {
+ data
+ imp {
+ key "exon" } ,
+ location
+ int {
+ from 298 ,
+ to 373 ,
+ id
+ gi 1234 } ,
+ qual {
+ {
+ qual "number" ,
+ val "25" } } } ,
+ {
+ data
+ imp {
+ key "intron" } ,
+ location
+ int {
+ from 374 ,
+ to 529 ,
+ id
+ gi 1234 } ,
+ qual {
+ {
+ qual "number" ,
+ val "25" } } } ,
+ {
+ data
+ imp {
+ key "exon" } ,
+ location
+ int {
+ from 530 ,
+ to 686 ,
+ id
+ gi 1234 } ,
+ qual {
+ {
+ qual "number" ,
+ val "26" } } } ,
+ {
+ data
+ imp {
+ key "misc_feature" } ,
+ comment "isotypic site" ,
+ location
+ int {
+ from 657 ,
+ to 674 ,
+ id
+ gi 1234 } } ,
+ {
+ data
+ imp {
+ key "intron" } ,
+ location
+ int {
+ from 687 ,
+ to 923 ,
+ id
+ gi 1234 } ,
+ qual {
+ {
+ qual "number" ,
+ val "26" } } } ,
+ {
+ data
+ imp {
+ key "exon" } ,
+ partial TRUE ,
+ location
+ int {
+ from 924 ,
+ to 944 ,
+ id
+ gi 1234 ,
+ fuzz-to
+ lim gt } ,
+ qual {
+ {
+ qual "number" ,
+ val "27" } } } ,
+ {
+ data
+ gene {
+ locus "C4" } ,
+ partial TRUE ,
+ location
+ int {
+ from 0 ,
+ to 944 ,
+ id
+ gi 1234 ,
+ fuzz-from
+ lim lt ,
+ fuzz-to
+ lim gt } } } } } } ,
+ seq {
+ id {
+ embl {
+ accession "CAA47393" ,
+ version 1 } ,
+ gi 1235 } ,
+ descr {
+ title "complement component C4, partial [Ovis aries]" ,
+ molinfo {
+ biomol peptide ,
+ completeness no-ends } ,
+ create-date
+ std {
+ year 1992 ,
+ month 7 ,
+ day 10 } } ,
+ inst {
+ repr raw ,
+ mol aa ,
+ length 129 ,
+ seq-data
+ ncbieaa "QGCGEQTMTLLAPTLAASRYLDKTEQWSLLPPETKDRAVDLIQKGYTRIQEFRKRDGSY
+GAWLHRDSSTWLTAFVLKILSLAQDQVGGSTKKLQETAMWLLSQQRDDGSFHDPCPVIHRDMQGGLVGSD" } ,
+ annot {
+ {
+ data
+ ftable {
+ {
+ data
+ prot {
+ name {
+ "complement component C4" } } ,
+ partial TRUE ,
+ location
+ int {
+ from 0 ,
+ to 128 ,
+ id
+ gi 1235 ,
+ fuzz-from
+ lim lt ,
+ fuzz-to
+ lim gt } } } } } } } ,
+ annot {
+ {
+ data
+ ftable {
+ {
+ data
+ cdregion {
+ frame two ,
+ code {
+ id 1 } } ,
+ partial TRUE ,
+ product
+ whole
+ gi 1235 ,
+ location
+ mix {
+ int {
+ from 0 ,
+ to 133 ,
+ id
+ gi 1234 ,
+ fuzz-from
+ lim lt } ,
+ int {
+ from 298 ,
+ to 373 ,
+ id
+ gi 1234 } ,
+ int {
+ from 530 ,
+ to 686 ,
+ id
+ gi 1234 } ,
+ int {
+ from 924 ,
+ to 944 ,
+ id
+ gi 1234 ,
+ fuzz-to
+ lim gt } } ,
+ dbxref {
+ {
+ db "GOA" ,
+ tag
+ str "Q29410" } ,
+ {
+ db "HSSP" ,
+ tag
+ str "1HZF" } ,
+ {
+ db "InterPro" ,
+ tag
+ str "IPR008930" } ,
+ {
+ db "InterPro" ,
+ tag
+ str "IPR011626" } ,
+ {
+ db "InterPro" ,
+ tag
+ str "IPR019565" } ,
+ {
+ db "UniProtKB/TrEMBL" ,
+ tag
+ str "Q29410" } } } } } } }
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/09d2462caebaea2d3ce67d4c52e717c7d30dcc7f
---
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/09d2462caebaea2d3ce67d4c52e717c7d30dcc7f
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