Autopkgtest: tests for gbseqget and nps2gps (09d2462c) · Commits · Debian Med / ncbi-tools6

debian/tests/run-unit-test

+15 −7

Original line number	Diff line number	Diff line
		@@ -115,6 +115,12 @@ end_out="$(grep -c "<Object-id_id>${last_id}</Object-id_id>" dsRNA_viruses.xgs)"
		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---'
		##################################################################
		@@ -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

0 → 100644

+457 −0

Original line number	Diff line number	Diff line
		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" } } } } } } }