genbank parser now compatible

bio/bio.go

@@ -18,6 +18,7 @@ import (
 
 	"github.com/TimothyStiles/poly/bio/fasta"
 	"github.com/TimothyStiles/poly/bio/fastq"
+	"github.com/TimothyStiles/poly/bio/genbank"
 	"github.com/TimothyStiles/poly/bio/pileup"
 	"github.com/TimothyStiles/poly/bio/slow5"
 	"golang.org/x/sync/errgroup"
@@ -29,6 +30,7 @@ type Format int
 const (
 	Fasta Format = iota
 	Fastq
+	Genbank
 	Slow5
 	Pileup
 )
@@ -41,10 +43,11 @@ const (
 // particular reason to use a different number.
 const defaultMaxLineLength int = bufio.MaxScanTokenSize // 64kB is a magic number often used by the Go stdlib for parsing.
 var DefaultMaxLengths = map[Format]int{
-	Fasta:  defaultMaxLineLength,
-	Fastq:  8 * 1024 * 1024,   // The longest single nanopore sequencing read so far is 4Mb. A 8mb buffer should be large enough for any sequencing.
-	Slow5:  128 * 1024 * 1024, // 128mb is used because slow5 lines can be massive, since a single read can be many millions of base pairs.
-	Pileup: defaultMaxLineLength,
+	Fasta:   defaultMaxLineLength,
+	Fastq:   8 * 1024 * 1024, // The longest single nanopore sequencing read so far is 4Mb. A 8mb buffer should be large enough for any sequencing.
+	Genbank: defaultMaxLineLength,
+	Slow5:   128 * 1024 * 1024, // 128mb is used because slow5 lines can be massive, since a single read can be many millions of base pairs.
+	Pileup:  defaultMaxLineLength,
 }
 
 /******************************************************************************
@@ -66,18 +69,22 @@ Lower level interfaces
 // for this is needed at the last Next(), when it returns an io.EOF error. A
 // pointer is used to represent the difference between a null DataType and an
 // empty DataType.
-type parserInterface[DataType fasta.Record | fastq.Read | slow5.Read | pileup.Line, DataTypeHeader fasta.Header | fastq.Header | slow5.Header | pileup.Header] interface {
+type parserInterface[DataType fasta.Record | fastq.Read | genbank.Genbank | slow5.Read | pileup.Line, DataTypeHeader fasta.Header | fastq.Header | genbank.Header | slow5.Header | pileup.Header] interface {
 	Header() (*DataTypeHeader, error)
 	Next() (*DataType, error)
 }
 
 // The following checks that all DataType and DataTypeHeaders implement the io.WriteTo interface.
 var _ io.WriterTo = (*fasta.Record)(nil)
 var _ io.WriterTo = (*fastq.Read)(nil)
+
+// genbank
 var _ io.WriterTo = (*slow5.Read)(nil)
 var _ io.WriterTo = (*pileup.Line)(nil)
 var _ io.WriterTo = (*fasta.Header)(nil)
 var _ io.WriterTo = (*fastq.Header)(nil)
+
+// genbank
 var _ io.WriterTo = (*slow5.Header)(nil)
 var _ io.WriterTo = (*pileup.Header)(nil)
 
@@ -90,7 +97,7 @@ Higher level parse
 // Parser is generic bioinformatics file parser. It contains a LowerLevelParser
 // and implements useful functions on top of it: such as Parse(), ParseToChannel(), and
 // ParseWithHeader().
-type Parser[DataType fasta.Record | fastq.Read | slow5.Read | pileup.Line, DataTypeHeader fasta.Header | fastq.Header | slow5.Header | pileup.Header] struct {
+type Parser[DataType fasta.Record | fastq.Read | genbank.Genbank | slow5.Read | pileup.Line, DataTypeHeader fasta.Header | fastq.Header | genbank.Header | slow5.Header | pileup.Header] struct {
 	parserInterface parserInterface[DataType, DataTypeHeader]
 }
 
@@ -116,6 +123,17 @@ func NewFastqParserWithMaxLineLength(r io.Reader, maxLineLength int) (*Parser[fa
 	return &Parser[fastq.Read, fastq.Header]{parserInterface: fastq.NewParser(r, maxLineLength)}, nil
 }
 
+// NewGenbankParser initiates a new Genbank parser form an io.Reader.
+func NewGenbankParser(r io.Reader) (*Parser[genbank.Genbank, genbank.Header], error) {
+	return NewGenbankParserWithMaxLineLength(r, DefaultMaxLengths[Genbank])
+}
+
+// NewGenbankParserWithMaxLineLength initiates a new Genbank parser from an
+// io.Reader and a user-given maxLineLength.
+func NewGenbankParserWithMaxLineLength(r io.Reader, maxLineLength int) (*Parser[genbank.Genbank, genbank.Header], error) {
+	return &Parser[genbank.Genbank, genbank.Header]{parserInterface: genbank.NewParser(r, maxLineLength)}, nil
+}
+
 // NewSlow5Parser initiates a new SLOW5 parser from an io.Reader.
 func NewSlow5Parser(r io.Reader) (*Parser[slow5.Read, slow5.Header], error) {
 	return NewSlow5ParserWithMaxLineLength(r, DefaultMaxLengths[Slow5])

bio/example_test.go

@@ -10,34 +10,8 @@ import (
 
 	"github.com/TimothyStiles/poly/bio"
 	"github.com/TimothyStiles/poly/bio/fasta"
-	"github.com/TimothyStiles/poly/bio/genbank"
-	"github.com/TimothyStiles/poly/bio/gff"
-	"github.com/TimothyStiles/poly/bio/polyjson"
 )
 
-// This is where the integration tests that make effed up cyclic dependencies go.
-func Example() {
-	// Poly can take in basic gff, gbk, fasta, and JSON.
-	// We call the json package "pson" (poly JSON) to prevent namespace collision with Go's standard json package.
-
-	gffInput, _ := gff.Read("../data/ecoli-mg1655-short.gff")
-	gbkInput, _ := genbank.Read("../data/puc19.gbk")
-	//fastaInput, _ := fasta.Read("fasta/data/base.fasta")
-	jsonInput, _ := polyjson.Read("../data/cat.json")
-
-	// Poly can also output these file formats. Every file format has a corresponding Write function.
-	_ = gff.Write(gffInput, "test.gff")
-	_ = genbank.Write(gbkInput, "test.gbk")
-	//_ = fasta.WriteFile(fastaInput, "test.fasta")
-	_ = polyjson.Write(jsonInput, "test.json")
-
-	// Extra tips:
-
-	// 1. All of these file formats can be read and written in JSON format using their native schemas.
-	// 2. If you want to convert from one format to another (e.g. genbank to polyjson), you can easily do so with a for-loop and some field mapping.
-	// 3. Every file format is unique but they all share a common interface so you can use them with almost every native function in Poly.
-}
-
 // ExampleRead shows an example of reading a file from disk.
 func ExampleRead() {
 	// Read lets you read files from disk into a parser.
@@ -50,8 +24,8 @@ func ExampleRead() {
 	// Output: ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK*
 }
 
+// Example_readGz shows an example of reading and parsing a gzipped file.
 func Example_readGz() {
-	// ReadGz lets you read gzipped files into a parser.
 	fileGz, _ := os.Open("fasta/data/base.fasta.gz")
 	file, _ := gzip.NewReader(fileGz)
 	parser, _ := bio.NewFastaParser(file)
@@ -200,6 +174,60 @@ $$&%&%#$)*59;/767C378411,***,('11<;:,0039/0&()&'2(/*((4.1.09751).601+'#&&&,-**/0
 	// Output:GATGTGCGCCGTTCCAGTTGCGACGTACTATAATCCCCGGCAACACGGTGCTGATTCTCTTCCTGTTCCAGAAAGCATAAACAGATGCAAGTCTGGTGTGATTAACTTCACCAAAGGGCTGGTTGTAATATTAGGAAATCTAACAATAGATTCTGTTGGTTGGACTCTAAAATTAGAAATTTGATAGATTCCTTTTCCCAAATGAAAGTTTAACGTACACTTTGTTTCTAAAGGAAGGTCAAATTACAGTCTACAGCATCGTAATGGTTCATTTTCATTTATATTTTAATACTAGAAAAGTCCTAGGTTGAAGATAACCACATAATAAGCTGCAACTTCAGCTGTCCCAACCTGAAGAAGAATCGCAGGAGTCGAAATAACTTCTGTAAAGCAAGTAGTTTGAACCTATTGATGTTTCAACATGAGCAATACGTAACT
 }
 
+func ExampleGenbankParser() {
+	// The following can be replaced with a any io.Reader. For example,
+	// `file, err := os.Open(path)` for file would also work.
+	file := strings.NewReader(`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
+//
+`)
+	parser, _ := bio.NewGenbankParser(file)
+	records, _ := parser.Parse()
+
+	fmt.Println(records[0].Features[2].Attributes["translation"])
+	// Output: MTMITPSLHACRSTLEDPRVPSSNSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRLMRYFLLTHLCGISHRIWCTLSTICSDAA
+}
+
 func ExampleNewSlow5Parser() {
 	// The following can be replaced with a any io.Reader. For example,
 	// `file, err := os.Open(path)` for file would also work.