Autopkgtest: tests for gbseqget and nps2gps

2 files changed, 472 insertions, 7 deletions

diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index 06056c47..d4e5f8f8 100644
--- 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 ]
diff --git a/debian/tests/test-data/idfetch_g1234.npset b/debian/tests/test-data/idfetch_g1234.npset
new file mode 100644
index 00000000..b06221de
--- /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" } } } } } } }