[med-svn] [Git][med-team/ncbi-tools6][master] Autopkgtest: tests for fa2htgs and spidey; test data files
Liubov Chuprikova
gitlab at salsa.debian.org
Mon May 21 23:14:55 BST 2018
Liubov Chuprikova pushed to branch master at Debian Med / ncbi-tools6
Commits:
30d017ce by Liubov Chuprikova at 2018-05-21T21:59:51+00:00
Autopkgtest: tests for fa2htgs and spidey; test data files
- - - - -
6 changed files:
- debian/copyright
- debian/source/include-binaries
- debian/tests/run-unit-test
- debian/tests/test-data/Sc_16.sbt
- + debian/tests/test-data/spidey_genome.fasta.gz
- + debian/tests/test-data/spidey_mRNA.fasta
Changes:
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -15,14 +15,18 @@ License: public_domain
Files: debian/tests/test-data/nc0225.aso.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/spidey_*
+Comment:
+ The sequences can be downloaded using their accession numbers with help of idfetch, e.g.:
+ idfetch -dn -t 5 -c 1 -g 1327850419 -o spidey_mRNA.fasta
+ idfetch -dn -t 5 -c 1 -g 568802167 -o spidey_genome.fasta
+
Files: debian/tests/test-data/trnascan-se_sample.output
Comment:
The file was generated by tRNAscan-SE 2.0:
@@ -30,8 +34,8 @@ Comment:
Files: debian/tests/test-data/Sc_16.*
Comment:
- The example of a template file can be found here:
- /usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz
+ The example of a template file was generated by NCBI Submission Portal:
+ https://submit.ncbi.nlm.nih.gov/genbank/template/submission/
.
The sequence and feature table examples were taken from here:
https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
=====================================
debian/source/include-binaries
=====================================
--- a/debian/source/include-binaries
+++ b/debian/source/include-binaries
@@ -1,3 +1,4 @@
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/test-data/spidey_genome.fasta.gz
=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -199,6 +199,10 @@ echo '---checksub test---'
/usr/bin/checksub -i Sc_16.sqn -o checksub.sqn
diff Sc_16.sqn checksub.sqn
+echo '---fa2htgs test---'
+/usr/bin/fa2htgs -i Sc_16.fsa -t Sc_16.sqn -n "Saccharomyces cerevisiae" -g mycenter -s ABC_1234567 -o fa2htgs.output -e fa2htgs.log
+[ -s fa2htgs.output ]
+
echo '---subfuse test---'
/usr/bin/subfuse -p ./ -o subfuse.output
[ -s subfuse.output ]
@@ -210,3 +214,7 @@ echo '---trna2tbl test---'
/usr/bin/trna2tbl < trnascan-se_sample.output > trna2tbl.output
[ -s trna2tbl.output ]
+echo '---spidey test---'
+/usr/bin/spidey -i spidey_genome.fasta -m spidey_mRNA.fasta -p 1 -o spidey.summary
+[ -s spidey.summary ]
+
=====================================
debian/tests/test-data/Sc_16.sbt
=====================================
--- a/debian/tests/test-data/Sc_16.sbt
+++ b/debian/tests/test-data/Sc_16.sbt
@@ -1,43 +1,139 @@
Submit-block ::= {
contact {
contact {
- name
- name {
- last "Darwin" ,
- first "Charles" ,
- initials "C.R." ,
- suffix "" } ,
- affil
- std {
- affil "Oxbridge University" ,
- div "Evolutionary Biology Department" ,
- city "Camford" ,
- country "United Kingdom" ,
- street "1859 Tennis Court Lane" ,
- email "darwin at beagle.edu.uk" ,
- phone "01 44 171-007-1212" ,
- postal-code "OX1 2BH" } } } ,
+ name name {
+ last "Darwin",
+ first "Charles",
+ middle "",
+ initials "",
+ suffix "",
+ title ""
+ },
+ affil std {
+ affil "Oxbridge University",
+ div "Evolutionary Biology Department",
+ city "Camford",
+ country "United Kingdom",
+ street "1859 Tennis Court Lane",
+ email "darwin at beagle.edu.uk",
+ phone "01 44 171-007-1212",
+ postal-code "OX1 2BH"
+ }
+ }
+ },
cit {
authors {
- names
- std {
+ names std {
+ {
+ name name {
+ last "Darwin",
+ first "Charles",
+ middle "",
+ initials "C.R.",
+ suffix "",
+ title ""
+ }
+ }
+ },
+ affil std {
+ affil "Oxbridge University",
+ div "Evolutionary Biology Department",
+ city "Camford",
+ country "United Kingdom",
+ street "1859 Tennis Court Lane",
+ postal-code "OX1 2BH"
+ }
+ }
+ },
+ subtype new
+}
+Seqdesc ::= pub {
+ pub {
+ sub {
+ authors {
+ names std {
{
- name
- name {
- last "Darwin" ,
- first "Charles" ,
- initials "C.R." } } } ,
- affil
- std {
- affil "Oxbridge University" ,
- div "Evolutionary Biology Department" ,
- city "Camford" ,
- country "United Kingdom" ,
- street "1859 Tennis Court Lane" ,
- postal-code "OX1 2BH" } } ,
- date
- std {
- year 2003 ,
- month 2 ,
- day 28 } } ,
- subtype new }
+ name ml "Darwin C",
+ }
+ },
+ affil str "Evolutionary Biology Department, Oxbridge University,
+ Camford, 1859 Tennis Court Lane, OX1 2BH, United Kingdom."
+ },
+ date std {
+ year 2018,
+ month 5,
+ day 19
+ },
+ },
+ article {
+ title {
+ name "In-depth analysis of one mysterious hypothetical protein of
+ Saccharomyces cerevisiae."
+ },
+ authors {
+ names std {
+ {
+ name ml "Darwin C",
+ affil str "Evolutionary Biology Department, Oxbridge University,
+ Camford, 1859 Tennis Court Lane, OX1 2BH, United Kingdom."
+ },
+ }
+ },
+ from journal {
+ title {
+ iso-jta "Nature",
+ ml-jta "Nature",
+ issn "1476-4687",
+ name "Nature"
+ },
+ imp {
+ date std {
+ year 2018,
+ month 5,
+ day 19
+ },
+ language "eng",
+ pubstatus aheadofprint,
+ history {
+ {
+ pubstatus other,
+ date std {
+ year 2018,
+ month 5,
+ day 21,
+ hour 6,
+ minute 0
+ }
+ }
+ }
+ }
+ },
+ ids {
+ pubmed 87654321,
+ doi "10.0000/tpj.12345",
+ other {
+ db "ELocationID doi",
+ tag str "10.0000/tpj.12345"
+ }
+ }
+ }
+ }
+}
+Seqdesc ::= user {
+ type str "Submission",
+ data {
+ {
+ label str "AdditionalComment",
+ data str "ALT EMAIL:darwin at beagle.edu.uk"
+ }
+ }
+}
+Seqdesc ::= user {
+ type str "Submission",
+ data {
+ {
+ label str "AdditionalComment",
+ data str "Submission Title:None"
+ }
+ }
+}
=====================================
debian/tests/test-data/spidey_genome.fasta.gz
=====================================
Binary files /dev/null and b/debian/tests/test-data/spidey_genome.fasta.gz differ
=====================================
debian/tests/test-data/spidey_mRNA.fasta
=====================================
--- /dev/null
+++ b/debian/tests/test-data/spidey_mRNA.fasta
@@ -0,0 +1,83 @@
+>gi|1327850419|ref|NM_017660.4| Homo sapiens GATA zinc finger domain containing 2A (GATAD2A), transcript variant 2, mRNA
+CTAGCAACCGGGGAAGCCGGGCTGTGAAGCGGGCAATTTCAGTGTGAGACTGAGCCGCGAGACTGAGCTG
+CGGCTCCGAGCGCTGCGCGGCGGCTCCTCCCGCCCAGGGTCAGCGCCCCGGCGCGCGCACGCGCACCCCC
+GCCGCCCGAGCGCGCCCCGCGCCGCCCGCGCAGTCGGTCGGTCGGTCGTCTGTCCTGTCGCCGCTGCCGC
+CGCCGCCACAGCGGCCGCCGCGGGCGCCACCTGAGGGAGTCGCCTCCGCGGGACGCCACAAGACCTGACC
+GGACTGCGCCGCCCGAGGCCGTCGGCCGCCGTCAGCGAGGGCGCCGAGCAACTTCGTTCAGAATGACCGA
+AGAAGCATGCCGAACACGGAGTCAGAAACGAGCGCTTGAACGGGACCCAACAGAGGACGATGTGGAGAGC
+AAGAAAATAAAAATGGAGAGAGGATTGTTGGCTTCAGATTTAAACACTGACGGAGACATGAGGGTGACAC
+CTGAGCCGGGAGCAGGTCCAACCCAAGGATTGCTGAGGGCAACAGAGGCCACGGCCATGGCCATGGGCAG
+AGGCGAAGGGCTGGTGGGCGATGGGCCCGTGGACATGCGCACCTCACACAGTGACATGAAGTCCGAGAGG
+AGACCCCCCTCACCTGACGTGATTGTGCTCTCCGACAACGAGCAGCCCTCGAGCCCGAGAGTGAATGGGC
+TGACCACGGTGGCCTTGAAGGAGACTAGCACCGAGGCCCTCATGAAAAGCAGTCCTGAAGAACGAGAAAG
+GATGATCAAGCAGCTGAAGGAAGAATTGAGGTTAGAAGAAGCAAAACTCGTGTTGTTGAAAAAGTTGCGG
+CAGAGTCAAATACAAAAGGAAGCCACCGCCCAGAAGCCCACAGGTTCTGTTGGGAGCACCGTGACCACCC
+CTCCCCCGCTTGTTCGGGGCACTCAGAACATTCCTGCTGGCAAGCCATCACTCCAGACCTCTTCAGCTCG
+GATGCCCGGCAGTGTCATACCCCCGCCCCTGGTCCGAGGTGGGCAGCAGGCGTCCTCGAAGCTGGGGCCA
+CAGGCGAGCTCACAGGTCGTCATGCCCCCACTCGTCAGGGGGGCTCAGCAAATCCACAGCATTAGGCAAC
+ATTCCAGCACAGGGCCACCGCCCCTCCTCCTGGCCCCCCGGGCGTCGGTGCCCAGTGTGCAGATTCAGGG
+ACAGAGGATCATCCAGCAGGGCCTCATCCGCGTCGCCAATGTTCCCAACACCAGCCTGCTCGTCAACATC
+CCACAGCCCACCCCAGCATCACTGAAGGGGACAACAGCCACCTCCGCTCAGGCCAACTCCACCCCCACTA
+GTGTGGCCTCTGTGGTCACCTCTGCCGAGTCTCCAGCAAGCCGACAGGCGGCCGCCAAGCTGGCGCTGCG
+CAAACAGCTGGAGAAGACGCTACTCGAGATCCCCCCACCCAAGCCCCCAGCCCCAGAGATGAACTTCCTG
+CCCAGCGCCGCCAACAACGAGTTCATCTACCTGGTCGGCCTGGAGGAGGTGGTGCAGAACCTACTGGAGA
+CACAAGGCAGGATGTCGGCCGCCACTGTGCTGTCCCGGGAGCCCTACATGTGTGCACAGTGCAAGACGGA
+CTTCACGTGCCGCTGGCGGGAGGAGAAGAGCGGCGCCATCATGTGTGAGAACTGCATGACAACCAACCAG
+AAGAAGGCGCTCAAGGTGGAGCACACCAGCCGGCTGAAGGCCGCCTTTGTGAAGGCGCTGCAGCAGGAAC
+AGGAGATTGAGCAGCGGCTCCTGCAGCAGGGCACGGCCCCTGCACAGGCCAAGGCCGAGCCCACCGCTGC
+CCCACACCCCGTGCTGAAGCAGGTCATAAAACCCCGGCGTAAGTTGGCGTTCCGCTCAGGAGAGGCCCGC
+GACTGGAGTAACGGGGCTGTGCTACAGGCCTCCAGCCAGCTGTCCCGGGGTTCGGCCACGACGCCCCGAG
+GTGTCCTGCACACGTTCAGTCCGTCACCCAAACTGCAGAACTCAGCCTCGGCCACAGCCCTGGTCAGCAG
+GACCGGCAGACATTCTGAGAGAACCGTGAGCGCCGGCAAGGGCAGCGCCACCTCCAACTGGAAGAAGACG
+CCCCTCAGCACAGGCGGGACCCTTGCGTTTGTCAGCCCAAGCCTGGCGGTGCACAAGAGCTCCTCGGCCG
+TGGACCGCCAGCGAGAGTACCTCCTGGACATGATCCCACCCCGCTCCATCCCCCAGTCAGCCACGTGGAA
+ATAGTGCGAGCCAGGCCCCGTGGAAGACGGGCTCCCTCCTCCCCCACCTGGCCCCTGGTCTAGAAGGACC
+CACTGCACCACCCTCCGCTGGCTCGGGAAGACACCGTGCCCGCCCCAAGAGCAAGCACCGGCCATGCTGC
+AGAGGCAAGACCTCAATTCTTGGCTGCAAAGTTTCATCAGGGCTAGGGGGCTGGTGCCGCCTCATAGGCA
+GACGAGGATCATCGCTGGGGGACCTTTCCCGTGGGCTTTCTTCCTTTCTCTCTTTGCCTTTAGTTTGCCC
+GACACCAGCAGAAAAGTGGACCTTGGGGGCTGGTTCTGCTCCTGGCCCCCTTGTTCAGCCCCTGCCGGCA
+CACGGGCGGCTCACCCTGGACACTGTGATGCGCATGGGCAAGGCCAGCGCCCGGGGCTTCTGAACCGAGC
+GGGGTGTTTCATTTTTTTGCTTTTCCCTGTCTTAGGCTCCCAGTCTTTGACTGCCTTCCCATGGCGATCT
+ATAAGTTGAAAGATTTTTTTTTTTTTTAATCACCTCATGATGATGGAGTTAAAAGTAAACCGTGCAGACC
+CTGGGGTCCCTGTTGTACGCTGCATCATCCCGCTGGCCCTGTGCCCTGGAGGGTGGGCGGCTCATGGTGC
+CACAGCCCCTGGCAGGGACGGCCGGCCCGCCCCCGTGACTGACTGACAGATGCAGGGATGGCCGAGGCAG
+CCCTCGCTCCAGCTGAACGCCTCCATTGCTGCTTGTTCTGGAGACCCCCGCCCCCGCACCTTCCAGACTT
+AGCAGAAGAACAAACTGAAGAACAGACCCAGCCAGAGAAGCAGGGATTCCAGAAGCTGCCCATTAAGGGA
+GAAGGAGAGGATCCGGTCGGCAGCAGCCCTGAGCAGAAAGCTGGAGGGGGGACTGTCGCGGGGTTTTTCT
+GTTGTGGTTTATTTTATTAAATTTTTTCCTTTTTTCTATTCATTTCGATGGACGCAATCTTAAGCCACCC
+TGGCCTTGCTCCTGGGAGGTGAGCGTGCACAGGTGTGTGCAGGTCAGGAGGTGCCGTCCAGGTGTGCGGC
+GAGCCGCTGCGCACAGATGTCAGGATTTCCGTTTGGGTCTAGTTTAGAACCTGTCCTTAAACCTAGGGGT
+TGCTGTCAGGATTTGCTTTCAGACTTTTTTTTTTTTTGTAATTCCCTTTAGAGTCTACAAAAATGTTTTT
+AAAAGGATCAGGTCTGCTTTTAGTTTCATTTTTGTTTCTTTCCCGTCCCACTCTTTAAAAACTGGTTCCG
+TGAGGAAAGGCAGAAGCCGTTCCGTGTCTCTTGCAGGCTGGGCCGGCTTCATGCCAGTGCGAGGGCGTCC
+CGTGCCCACGTACATACGTATGTCTCCATGAGTTCTGGGCTCCACTGGTTCCAATTGAGCTCCAGCCCTG
+GTTTTCCTACCCATGCAGTTAGGGACTTTAATTTAATTTTTTTTTTGTAGGGCCACCGCCTTCAAACACA
+ACTGCTACAACATTCTAATAAAGGCTCATTTAACCCCCAGGCTCCTGTCGTGTGAATATCCTCAGTCTGT
+AGGAAACTTTTTTTGACACAGCATAGAAGACCTAGTTTTGGAAAACATTATCTAATTTTTTGTTGTGCAA
+ATCCCCAAATTTCTCACTAATTTTTGTTTTTTTGTGCATAACTTGGATGGGCTGAAGGAGGTGAGGACAG
+ATTGGGGAAGGGTGGCTTTCATTCCAAGATCCAGGGATTTGGGGAAAAGGAAGGAATTTGATGTTTTTTG
+GGGTGGGAGGGGAGGGTGTGTTTTTTACACCAAAAAAAAAAAAAAAAATCAAGAGTATGCAAGCATTTCT
+ATTCCTCGCATTTTTCTGTGTGCCTGGCAAATAAATACCTGTCTCCTACGACCCTGAGCTGTTAGCCCTC
+TCTGTTCCATGACAGGGGCCAGATCTTCCAGCTCCTCCCAGAAGGAGCACCCAGGCTGGCTTCTTCCCAC
+TGAAAGCCCTCCCCAGCGAACCAACCTCAGTTCTATGCAGTGGCTGGGGATCAGGCATCCAGACCGAAGT
+CACCTCTGCCTGCTCCAGCTTGGGTCAGCTGGGTCTGACCAGGGGGCCAGATCCGAGCCGCACCTGCCGG
+CCCCCAGCCCCAGCTCCAGCTCCTGACCTCTCCCAGCCTGGCCTGGCTGTTCCTCCAGGGCTGATGGCTG
+TCAACCCATCCTTGTGAGTTCATATGGACTGCTGCCCCTCGAAAGGGAGAGGGTCGGCCCCATGTCCCCA
+GGGAGCATTCCATCAGGGACAACGTACATACTGTGATGTAAACTTTTTTTTTTTCCCCCCAGGGGGCAAA
+AGTGTGAGATGCCTTAATCTTTCCTTCATTTCTGCTGTCTCGAACACTCTAGCCCATTATTTCCTTTCAG
+TTCCTTGCAGCATAACCTCTACGATAAGCCCCAAGCGGGTTGTTGTATTATGACGTTTATGATGTTCCAG
+GTGAAGGCATTATTAAGTACCTCTCTGGGTGTGGGGTTTGGACGCACCAGGATAGCTATTGATTAATGTT
+AAGGGTGTTCTACCCACAGCAAAGCACACCCTCTTAAACCAGGCACTGCCTGGGTCCTGGTCCCGAGAGC
+CCTACCAGGATCAGGTTCCTGCAAGCCGTCAGAATGTGGGAGCCCCCAGCCCAACTGATTGTAACTGTCC
+CCTGTTACCTGTGACATGAACCTCCAACAGCACCTGGAAACGGTTCCCTCTGTCAGCTGCTCTGTAGACA
+GGGCTGGGGAGATCTCAGAGTTCACACCTCGCCTGTTGTAGGGGAGGTTGGGGGTAGGGTTTGGAATGGC
+CAAGTGCCCTTGGAACCTCCCACAGCTATGGCCGTCCTGACCTCATCCCAGGAACTCTACGGTGACCAGG
+AACCACCCCTCTGACGAGGTCTGTAGCGGCCCTTCTCAGAGTGGAACAGCCCACAGTGCTAGTTGTGCCT
+GGTCTTACCTGTACTCCACGGACCTCGGTGAAGCAAAAGCTTCAGGGCAGAGGGAATGAGGCAACCCAGT
+GGCAGCCCCGCTGGGCCCCGTGGCTCCTGCTCTCCTATTGGACGTAGAGGCAGGGGAGAGACTTCTCTAT
+ACAAATATTCTCATCACAGAAGGGATGATCCTTGCTGCTCTGCCGTAGGGTTTTTGATGCTGAGCTATGC
+TGCACATGACGTTAACCTAAAGAACTTGGACTGAGCTTTTAAAAAAGGACAGCAAACAATTTTATAATCC
+TTAAAGTGTAATAGACGGTTACACTAGTGCAGGGTATTGGGGAGGCTCTTTGGGTGTGGAGGCTGTCACT
+TGTATTTATTGTGACTCTAAATCTTTGATAGTAAAACAAATGTAAAAAGAAATGTTTGCCACCAGATGGG
+AATAGAAGTTCCAATAAGCAGGCTGGAATGGGTGGCTATACGTTGTATCACGAGGAAGTTTTAGACTCTG
+AAGGATAATAAATGGATGATGTGTCAACTGGAAAAAAAAAAAAAAAAAA
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/30d017ce626df4304da578106c6c15fd3b7f7088
---
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/commit/30d017ce626df4304da578106c6c15fd3b7f7088
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