Autopkgtest: tests for fa2htgs and spidey; test data files (30d017ce) · Commits · Debian Med / ncbi-tools6

debian/copyright

+8 −4

Original line number	Diff line number	Diff line
		@@ -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

+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/test-data/spidey_genome.fasta.gz

debian/tests/run-unit-test

+8 −0

Original line number	Diff line number	Diff line
		@@ -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

+133 −37

Original line number	Diff line number	Diff line
		Submit-block ::= {
		contact {
		contact {
		name
		name {
		name name {
		last "Darwin",
		first "Charles",
		initials "C.R." ,
		suffix "" } ,
		affil
		std {
		middle "",
		initials "",
		suffix "",
		title ""
		},
		affil std {
		affil "Oxbridge University",
		div "Evolutionary Biology Department",
		city "Camford",
		@@ -16,28 +17,123 @@ Submit-block ::= {
		street "1859 Tennis Court Lane",
		email "darwin@beagle.edu.uk",
		phone "01 44 171-007-1212",
		postal-code "OX1 2BH" } } } ,
		postal-code "OX1 2BH"
		}
		}
		},
		cit {
		authors {
		names
		std {
		names std {
		{
		name
		name {
		name name {
		last "Darwin",
		first "Charles",
		initials "C.R." } } } ,
		affil
		std {
		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" } } ,
		date
		std {
		year 2003 ,
		month 2 ,
		day 28 } } ,
		subtype new }
		postal-code "OX1 2BH"
		}
		}
		},
		subtype new
		}
		Seqdesc ::= pub {
		pub {
		sub {
		authors {
		names std {
		{
		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@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

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