Updated with Genbank in spec.yaml

Koeng101 · Dec 10, 2023 · e26c6b9 · e26c6b9
1 parent 71800fb
commit e26c6b9
Show file tree

Hide file tree

Showing 16 changed files with 1,173 additions and 808 deletions.
diff --git a/api/api/api.go b/api/api/api.go
@@ -93,6 +93,7 @@ func InitializeApp() App {
 
 	// IO handlers.
 	app.Router.HandleFunc("/api/io/fasta/parse", appImpl.PostIoFastaParse)
+	app.Router.HandleFunc("/api/io/genbank/parse", appImpl.PostIoGenbankParse)
 
 	// CDS design handlers.
 	app.Router.HandleFunc("/api/design/cds/fix", appImpl.PostDesignCdsFix)
@@ -145,11 +146,32 @@ func (app *App) PostIoFastaParse(ctx context.Context, request gen.PostIoFastaPar
 	}
 	data := make([]gen.FastaRecord, len(fastas))
 	for i, fastaRecord := range fastas {
-		data[i] = gen.FastaRecord{Name: fastaRecord.Identifier, Sequence: fastaRecord.Sequence}
+		data[i] = gen.FastaRecord(*fastaRecord)
 	}
 	return gen.PostIoFastaParse200JSONResponse(data), nil
 }
 
+func (app *App) PostIoGenbankParse(ctx context.Context, request gen.PostIoGenbankParseRequestObject) (gen.PostIoGenbankParseResponseObject, error) {
+	genbankString := *request.Body
+	parser, err := bio.NewGenbankParser(strings.NewReader(genbankString + "\n"))
+	if err != nil {
+		return gen.PostIoGenbankParse500TextResponse(fmt.Sprintf("Got error: %s", err)), nil
+	}
+	genbanks, err := parser.Parse()
+	if err != nil {
+		return gen.PostIoGenbankParse500TextResponse(fmt.Sprintf("Got error: %s", err)), nil
+	}
+	data := make([]gen.GenbankRecord, len(genbanks))
+	for i, genbankRecord := range genbanks {
+		err := genbankRecord.StoreFeatureSequences()
+		if err != nil {
+			return gen.PostIoGenbankParse500TextResponse(fmt.Sprintf("Got error: %s", err)), nil
+		}
+		data[i] = gen.GenbankRecord(*genbankRecord)
+	}
+	return gen.PostIoGenbankParse200JSONResponse(data), nil
+}
+
 /*
 *****************************************************************************
 

diff --git a/api/api/api_test.go b/api/api/api_test.go
@@ -32,7 +32,62 @@ IENY
 	resp := httptest.NewRecorder()
 	app.Router.ServeHTTP(resp, req)
 
-	r := `[{"name":"gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]","sequence":"LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY"}]`
+	r := `[{"identifier":"gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]","sequence":"LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY"}]`
+	if strings.TrimSpace(resp.Body.String()) != r {
+		t.Errorf("Unexpected response. Expected: " + r + "\nGot: " + resp.Body.String())
+	}
+}
+
+func TestIoGenbankParse(t *testing.T) {
+	baseGenbank := `LOCUS       pUC19_lacZ         336 bp DNA     linear   UNA 12-SEP-2023
+DEFINITION  natural linear DNA
+ACCESSION   .
+VERSION     .
+KEYWORDS    .
+SOURCE      natural DNA sequence
+  ORGANISM  unspecified
+REFERENCE   1  (bases 1 to 336)
+  AUTHORS   Keoni Gandall
+  TITLE     Direct Submission
+  JOURNAL   Exported Sep 12, 2023 from SnapGene 6.2.2
+            https://www.snapgene.com
+FEATURES             Location/Qualifiers
+     source          1..336
+                     /mol_type="genomic DNA"
+                     /organism="unspecified"
+     primer_bind     1..17
+                     /label=M13 rev
+                     /note="common sequencing primer, one of multiple similar
+                     variants"
+     CDS             13..336
+                     /codon_start=1
+                     /gene="lacZ"
+                     /product="LacZ-alpha fragment of beta-galactosidase"
+                     /label=lacZ-alpha
+                     /translation="MTMITPSLHACRSTLEDPRVPSSNSLAVVLQRRDWENPGVTQLNR
+                     LAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRLMRYFLLTHLCGISHRIWCTLSTICS
+                     DAA"
+     misc_feature    30..86
+                     /label=MCS
+                     /note="pUC19 multiple cloning site"
+     primer_bind     complement(87..103)
+                     /label=M13 fwd
+                     /note="common sequencing primer, one of multiple similar
+                     variants"
+ORIGIN
+        1 caggaaacag ctatgaccat gattacgcca agcttgcatg cctgcaggtc gactctagag
+       61 gatccccggg taccgagctc gaattcactg gccgtcgttt tacaacgtcg tgactgggaa
+      121 aaccctggcg ttacccaact taatcgcctt gcagcacatc cccctttcgc cagctggcgt
+      181 aatagcgaag aggcccgcac cgatcgccct tcccaacagt tgcgcagcct gaatggcgaa
+      241 tggcgcctga tgcggtattt tctccttacg catctgtgcg gtatttcaca ccgcatatgg
+      301 tgcactctca gtacaatctg ctctgatgcc gcatag
+//
+`
+	req := httptest.NewRequest("POST", "/api/io/genbank/parse", strings.NewReader(baseGenbank))
+	resp := httptest.NewRecorder()
+	app.Router.ServeHTTP(resp, req)
+
+	r := `[{"features":[{"attributes":{"mol_type":["genomic DNA"],"organism":["unspecified"]},"description":"","location":{"complement":false,"end":336,"fivePrimePartial":false,"gbkLocationString":"","join":false,"start":0,"subLocations":null,"threePrimePartial":false},"sequence":"caggaaacagctatgaccatgattacgccaagcttgcatgcctgcaggtcgactctagaggatccccgggtaccgagctcgaattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcctgatgcggtattttctccttacgcatctgtgcggtatttcacaccgcatatggtgcactctcagtacaatctgctctgatgccgcatag","sequenceHash":"","sequenceHashFunction":"","type":"source"},{"attributes":{"label":["M13 rev"],"note":["common sequencing primer, one of multiple similarvariants"]},"description":"","location":{"complement":false,"end":17,"fivePrimePartial":false,"gbkLocationString":"","join":false,"start":0,"subLocations":null,"threePrimePartial":false},"sequence":"caggaaacagctatgac","sequenceHash":"","sequenceHashFunction":"","type":"primer_bind"},{"attributes":{"codon_start":["1"],"gene":["lacZ"],"label":["lacZ-alpha"],"product":["LacZ-alpha fragment of beta-galactosidase"],"translation":["MTMITPSLHACRSTLEDPRVPSSNSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRLMRYFLLTHLCGISHRIWCTLSTICSDAA"]},"description":"","location":{"complement":false,"end":336,"fivePrimePartial":false,"gbkLocationString":"","join":false,"start":12,"subLocations":null,"threePrimePartial":false},"sequence":"atgaccatgattacgccaagcttgcatgcctgcaggtcgactctagaggatccccgggtaccgagctcgaattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcctgatgcggtattttctccttacgcatctgtgcggtatttcacaccgcatatggtgcactctcagtacaatctgctctgatgccgcatag","sequenceHash":"","sequenceHashFunction":"","type":"CDS"},{"attributes":{"label":["MCS"],"note":["pUC19 multiple cloning site"]},"description":"","location":{"complement":false,"end":86,"fivePrimePartial":false,"gbkLocationString":"","join":false,"start":29,"subLocations":null,"threePrimePartial":false},"sequence":"aagcttgcatgcctgcaggtcgactctagaggatccccgggtaccgagctcgaattc","sequenceHash":"","sequenceHashFunction":"","type":"misc_feature"},{"attributes":{"label":["M13 fwd"],"note":["common sequencing primer, one of multiple similarvariants"]},"description":"","location":{"complement":true,"end":103,"fivePrimePartial":false,"gbkLocationString":"complement(87..103)","join":false,"start":86,"subLocations":null,"threePrimePartial":false},"sequence":"gtaaaacgacggccagt","sequenceHash":"","sequenceHashFunction":"","type":"primer_bind"}],"meta":{"accession":".","baseCount":null,"date":"","definition":"natural linear DNA","keywords":".","locus":{"circular":false,"genbankDivision":"UNA","modificationDate":"12-SEP-2023","moleculeType":"DNA","name":"pUC19_lacZ","sequenceCoding":"bp","sequenceLength":"336"},"name":"","organism":"unspecified","origin":"","other":{},"references":[{"authors":"Keoni Gandall","consortium":"","journal":"Exported Sep 12, 2023 from SnapGene 6.2.2 https://www.snapgene.com","pubMed":"","range":"(bases 1 to 336)","remark":"","title":"Direct Submission"}],"sequenceHash":"","sequenceHashFunction":"","source":"natural DNA sequence","taxonomy":null,"version":"."},"sequence":"caggaaacagctatgaccatgattacgccaagcttgcatgcctgcaggtcgactctagaggatccccgggtaccgagctcgaattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcctgatgcggtattttctccttacgcatctgtgcggtatttcacaccgcatatggtgcactctcagtacaatctgctctgatgccgcatag"}]`
 	if strings.TrimSpace(resp.Body.String()) != r {
 		t.Errorf("Unexpected response. Expected: " + r + "\nGot: " + resp.Body.String())
 	}