Add fasta2 package

io/fasta2/example_test.go

@@ -0,0 +1,15 @@
+package fasta2_test
+
+import (
+	"fmt"
+
+	"github.com/TimothyStiles/poly/io/fasta2"
+)
+
+// ExampleReadFile shows basic usage for ReadFile
+func ExampleReadFile() {
+	fastas, _ := fasta2.ReadFile("testdata/base.fasta")
+
+	fmt.Println(fastas[0].Header)
+	// Output: gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
+}

io/fasta2/fasta.go

@@ -0,0 +1,85 @@
+package fasta2
+
+import (
+	"bytes"
+	"fmt"
+	"io"
+	"os"
+)
+
+// Record is a struct representing a single Record element with a Name and its corresponding Sequence.
+type Record struct {
+	Header   string `json:"header"`
+	Sequence string `json:"sequence"`
+}
+
+// buffer is a utility method to serialize the Record in a buffer.
+func (r Record) buffer() bytes.Buffer {
+	var b bytes.Buffer
+	// grow the buffer to allocate just once, the numbers are in order:
+	// the header + > + \n, the sequence + one \n for each 80 char, the last \n
+	b.Grow(len(r.Header) + 2 + len(r.Sequence) + (len(r.Sequence) % 80) + 1)
+	b.WriteByte('>')
+	b.WriteString(r.Header)
+	for i, c := range r.Sequence {
+		// write the fasta sequence 80 characters at a time
+		if i%80 == 0 {
+			b.WriteByte('\n')
+		}
+		b.WriteRune(c)
+	}
+	b.WriteByte('\n')
+
+	return b
+}
+
+// returns the string representation of a Record.
+func (r Record) String() string {
+	b := r.buffer()
+	return b.String()
+}
+
+// returns the representation of a Record as []byte.
+func (r Record) Bytes() []byte {
+	b := r.buffer()
+	return b.Bytes()
+}
+
+// Writes the Record []byte representation to the passed io.Writer.
+func (r Record) Write(w io.Writer) error {
+	recBytes := r.Bytes()
+	_, err := w.Write(recBytes)
+	if err != nil {
+		return fmt.Errorf("error writing record to io.Writer: %w", err)
+	}
+
+	return nil
+}
+
+// Write writes a fasta array to an io.Writer
+func Write(recs []Record, w io.Writer) error {
+	for _, r := range recs {
+		err := r.Write(w)
+		if err != nil {
+			return err
+		}
+	}
+	return nil
+}
+
+// WriteFile writes all the passed records to the file at path.
+func WriteFile(recs []Record, path string) error {
+	f, err := os.Create(path)
+	if err != nil {
+		return fmt.Errorf("error opening file %q: %w", path, err)
+	}
+	defer f.Close()
+	for _, r := range recs {
+		err := r.Write(f)
+		if err != nil {
+			return fmt.Errorf("error writing to file %q: %w", path, err)
+		}
+	}
+
+	return nil
+}

io/fasta2/fasta_test.go

@@ -0,0 +1,146 @@
+package fasta2_test
+
+import (
+	"bytes"
+	"io"
+	"os"
+	"path"
+	"reflect"
+	"testing"
+
+	"github.com/TimothyStiles/poly/io/fasta2"
+	"github.com/stretchr/testify/require"
+)
+
+func TestFastaString(t *testing.T) {
+	type fields struct {
+		Header   string
+		Sequence string
+	}
+	tests := []struct {
+		header string
+		fields fields
+		want   string
+	}{
+		{
+			header: "success",
+			fields: fields{
+				Header:   "Cool Sequence",
+				Sequence: "MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSSEMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL",
+			},
+			want: ">Cool Sequence\nMDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSSEMFNEFDKRYAQGKGF\nITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL\n",
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.header, func(t *testing.T) {
+			f := fasta2.Record{
+				Header:   tt.fields.Header,
+				Sequence: tt.fields.Sequence,
+			}
+			if got := f.String(); got != tt.want {
+				t.Errorf("Record.String() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func TestRecord_Bytes(t *testing.T) {
+	type fields struct {
+		Header   string
+		Sequence string
+	}
+	tests := []struct {
+		name   string
+		fields fields
+		want   []byte
+	}{
+		{
+			name: "success",
+			fields: fields{
+				Header:   "Cool Sequence",
+				Sequence: "MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSSEMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL",
+			},
+			want: []byte(">Cool Sequence\nMDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSSEMFNEFDKRYAQGKGF\nITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL\n"),
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			r := fasta2.Record{
+				Header:   tt.fields.Header,
+				Sequence: tt.fields.Sequence,
+			}
+			if got := r.Bytes(); !reflect.DeepEqual(got, tt.want) {
+				t.Errorf("Record.Bytes() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func TestRecordWrite(t *testing.T) {
+	sequence := fasta2.Record{
+		Header:   "Cool Sequence",
+		Sequence: "MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSSEMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL",
+	}
+	expected := ">Cool Sequence\nMDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSSEMFNEFDKRYAQGKGF\nITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL\n"
+	t.Run("success", func(t *testing.T) {
+		r := sequence
+		w := &bytes.Buffer{}
+		err := r.Write(w)
+		require.NoError(t, err)
+		require.Equal(t, expected, w.String())
+	})
+	t.Run("fail truncated", func(t *testing.T) {
+		r := sequence
+		w := errorWriter{}
+		err := r.Write(w)
+		require.Error(t, err)
+	})
+}
+
+func TestWrite(t *testing.T) {
+	recs := []fasta2.Record{
+		{
+			Header:   "name1",
+			Sequence: "seq1",
+		},
+		{
+			Header:   "name2",
+			Sequence: "seq2",
+		},
+	}
+	t.Run("success", func(t *testing.T) {
+		w := &bytes.Buffer{}
+		err := fasta2.Write(recs, w)
+		require.NoError(t, err)
+		require.Equal(t, ">name1\nseq1\n>name2\nseq2\n", w.String())
+	})
+	t.Run("fail EOF", func(t *testing.T) {
+		w := errorWriter{}
+		err := fasta2.Write(recs, w)
+		require.Error(t, err)
+	})
+}
+
+func TestWriteFile(t *testing.T) {
+	path := path.Join(os.TempDir(), "fasta_test")
+	defer os.Remove(path) // clean up
+	recs := []fasta2.Record{
+		{
+			Header:   "name1",
+			Sequence: "seq1",
+		},
+		{
+			Header:   "name2",
+			Sequence: "seq2",
+		},
+	}
+	err := fasta2.WriteFile(recs, path)
+	require.NoError(t, err)
+}
+
+// errorWriter is a test utility to have errors
+type errorWriter struct{}
+
+func (ew errorWriter) Write(p []byte) (n int, err error) {
+	return len(p), io.EOF
+}

io/fasta2/parser.go

@@ -0,0 +1,128 @@
+package fasta2
+
+import (
+	"bufio"
+	"bytes"
+	"fmt"
+	"io"
+	"os"
+)
+
+// Parser is a fasta parser it is initialized by the NewParser() function.
+type Parser struct {
+	buff    bytes.Buffer
+	header  string
+	start   bool
+	scanner *bufio.Scanner
+	line    int
+	more    bool
+}
+
+func NewParser(r io.Reader) *Parser {
+	return &Parser{
+		start:   true,
+		more:    true,
+		scanner: bufio.NewScanner(r),
+	}
+}
+
+// Lines returns the number of lines parsed.
+func (p *Parser) Lines() int {
+	return p.line
+}
+
+// HasNext returns true if the parser can continue parsing.
+func (p *Parser) HasNext() bool {
+	return p.more
+}
+
+func (p *Parser) newRecord() Record {
+	sequence := p.buff.String()
+	record := Record{
+		Header:   p.header,
+		Sequence: sequence,
+	}
+	// Reset sequence buffer
+	p.buff.Reset()
+	return record
+}
+
+// Next parsed the next record in the io.Reader and returns it, in case
+// something went wrong an error and the partial result is returned.
+func (p *Parser) Next() (Record, error) {
+	for p.scanner.Scan() {
+		line := p.scanner.Bytes()
+		p.line++
+		switch {
+		// if there's nothing on this line skip this iteration of the loop
+		case len(line) == 0:
+			continue
+		// if it's a comment skip this line
+		case line[0] == ';':
+			continue
+		// start of file with no header, error
+		case line[0] != '>' && p.start:
+			err := fmt.Errorf("invalid input: missing sequence header for sequence starting at line %d", p.line)
+			record := p.newRecord()
+			return record, err
+		// start of a fasta line
+		case line[0] != '>':
+			p.buff.Write(line)
+		// Process normal new lines
+		case line[0] == '>' && !p.start:
+			record := p.newRecord()
+			// New name
+			p.header = string(line[1:])
+			return record, nil
+		// Process first line of file
+		case line[0] == '>' && p.start:
+			p.header = string(line[1:])
+			p.start = false
+		}
+	}
+	p.more = false
+	// Add final sequence in file
+	record := p.newRecord()
+	return record, p.scanner.Err()
+}
+
+// ParseAll will parse all the records found in the reader and returns them in
+// a slice.
+func ParseAll(r io.Reader) ([]Record, error) {
+	var (
+		ret []Record
+		p   = NewParser(r)
+	)
+
+	for p.HasNext() {
+		rec, err := p.Next()
+		if err != nil {
+			return ret, err
+		}
+		ret = append(ret, rec)
+	}
+
+	return ret, nil
+}
+
+// ReadFile will parse all the records found in the file and returns them in
+// a slice.
+func ReadFile(path string) ([]Record, error) {
+	var ret []Record
+	f, err := os.Open(path)
+	if err != nil {
+		return nil, fmt.Errorf("error while reading file %q: %w", path, err)
+	}
+	defer f.Close()
+
+	p := NewParser(f)
+	for p.HasNext() {
+		rec, err := p.Next()
+		if err != nil {
+			return ret, err
+		}
+		ret = append(ret, rec)
+	}
+
+	return ret, nil
+}