github.com/biogo/biogo@v1.0.4/io/featio/gff/gff_test.go

// Copyright ©2011-2012 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.

package gff

import (
	"github.com/biogo/biogo/alphabet"
	"github.com/biogo/biogo/feat"
	"github.com/biogo/biogo/seq"
	"github.com/biogo/biogo/seq/linear"

	"bytes"
	"io"
	"strings"
	"testing"
	"time"

	"gopkg.in/check.v1"
)

// Helpers
func floatPtr(f float64) *float64 { return &f }

func mustTime(t time.Time, err error) time.Time {
	if err != nil {
		panic(err)
	}
	return t
}

// Tests
func Test(t *testing.T) { check.TestingT(t) }

type S struct{}

var _ = check.Suite(&S{})

var (
	gffTests = []struct {
		gff  string
		feat []*Feature
	}{
		{
			gff: `SEQ1	EMBL	atg	103	105	.	+	0
SEQ1	EMBL	exon	103	172	.	+	0
SEQ1	EMBL	splice5	172	173	.	+	.
SEQ1	netgene	splice5	172	173	0.94	+	.
SEQ1	genie	sp5-20	163	182	2.3	+	.
SEQ1	genie	sp5-10	168	177	2.1	+	.
SEQ2	grail	ATG	17	19	2.1	-	0
`,
			feat: []*Feature{
				{SeqName: "SEQ1", Source: "EMBL", Feature: "atg", FeatStart: 102, FeatEnd: 105, FeatScore: nil, FeatFrame: Frame0, FeatStrand: seq.Plus},
				{SeqName: "SEQ1", Source: "EMBL", Feature: "exon", FeatStart: 102, FeatEnd: 172, FeatScore: nil, FeatFrame: Frame0, FeatStrand: seq.Plus},
				{SeqName: "SEQ1", Source: "EMBL", Feature: "splice5", FeatStart: 171, FeatEnd: 173, FeatScore: nil, FeatFrame: NoFrame, FeatStrand: seq.Plus},
				{SeqName: "SEQ1", Source: "netgene", Feature: "splice5", FeatStart: 171, FeatEnd: 173, FeatScore: floatPtr(0.94), FeatFrame: NoFrame, FeatStrand: seq.Plus},
				{SeqName: "SEQ1", Source: "genie", Feature: "sp5-20", FeatStart: 162, FeatEnd: 182, FeatScore: floatPtr(2.3), FeatFrame: NoFrame, FeatStrand: seq.Plus},
				{SeqName: "SEQ1", Source: "genie", Feature: "sp5-10", FeatStart: 167, FeatEnd: 177, FeatScore: floatPtr(2.1), FeatFrame: NoFrame, FeatStrand: seq.Plus},
				{SeqName: "SEQ2", Source: "grail", Feature: "ATG", FeatStart: 16, FeatEnd: 19, FeatScore: floatPtr(2.1), FeatFrame: Frame0, FeatStrand: seq.Minus},
			},
		},
	}

	metaTests = []struct {
		date          string
		format        string
		sourceVersion string
		version       int
		name          string
		molType       feat.Moltype
		gff           string
		feat          []feat.Feature
		write         []interface{}
	}{
		{
			date:          "1997-11-08",
			format:        Astronomical,
			sourceVersion: "<source> <version-text>",
			version:       2,
			name:          "<seqname>",
			molType:       feat.DNA,

			gff: `##gff-version 2
##source-version <source> <version-text>
##date 1997-11-08
##Type DNA <seqname>
##DNA <seqname>
##acggctcggattggcgctggatgatagatcagacgac
##...
##end-DNA
##RNA <seqname>
##acggcucggauuggcgcuggaugauagaucagacgac
##...
##end-RNA
##Protein <seqname>
##MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF
##...
##end-Protein
##sequence-region <seqname> 1 5
`,
			feat: []feat.Feature{
				linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggctcggattggcgctggatgatagatcagacgac...")), alphabet.DNA),
				linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggcucggauuggcgcuggaugauagaucagacgac...")), alphabet.RNA),
				linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF...")), alphabet.Protein),
				&Region{Sequence: Sequence{SeqName: "<seqname>", Type: feat.DNA}, RegionStart: 0, RegionEnd: 5},
			},
			write: []interface{}{
				2,
				"source-version <source> <version-text>",
				mustTime(time.Parse(Astronomical, "1997-11-08")),
				Sequence{SeqName: "<seqname>", Type: feat.DNA},
				linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggctcggattggcgctggatgatagatcagacgac...")), alphabet.DNA),
				linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("acggcucggauuggcgcuggaugauagaucagacgac...")), alphabet.RNA),
				linear.NewSeq("<seqname>", alphabet.BytesToLetters([]byte("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF...")), alphabet.Protein),
				&Region{Sequence: Sequence{SeqName: "<seqname>"}, RegionStart: 0, RegionEnd: 5},
			},
		},
	}
)

func (s *S) TestUnsafeString(c *check.C) {
	for _, t := range []string{
		"I",
		"Lorem",
		"Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.",
	} {
		b := []byte(t)
		c.Check(unsafeString(b), check.Equals, t)
	}
}

func (s *S) TestReadGFF(c *check.C) {
	for i, g := range gffTests {
		buf := strings.NewReader(g.gff)
		r := NewReader(buf)
		for j := 0; ; j++ {
			f, err := r.Read()
			if err == io.EOF {
				c.Check(j, check.Equals, len(g.feat))
				break
			}
			c.Check(f, check.DeepEquals, g.feat[j], check.Commentf("Test: %d Line: %d", i, j+1))
			c.Check(err, check.Equals, nil)
		}
	}
}

func (s *S) TestReadMetaline(c *check.C) {
	for i, g := range metaTests {
		buf := strings.NewReader(g.gff)
		r := NewReader(buf)
		for j := 0; ; j++ {
			f, err := r.Read()
			if err == io.EOF {
				c.Check(j, check.Equals, len(g.feat))
				break
			}
			c.Check(f, check.DeepEquals, g.feat[j], check.Commentf("Test: %d Line: %d", i, j+1))
			c.Check(err, check.Equals, nil)
		}
		c.Check(r.Version, check.Equals, g.version)
		date, err := time.Parse(g.format, g.date)
		c.Assert(err, check.Equals, nil)
		c.Check(r.Name, check.Equals, g.name)
		c.Check(r.Type, check.Equals, g.molType)
		c.Check(r.Date, check.Equals, date)
		c.Check(r.SourceVersion, check.Equals, g.sourceVersion)
	}
}

const width = 37 // Not the normal fasta width - this matches the examples from the GFF spec page.

func (s *S) TestWriteGff(c *check.C) {
	for i, g := range gffTests {
		buf := &bytes.Buffer{}
		w := NewWriter(buf, width, false)
		var n int
		for _, f := range g.feat {
			_n, err := w.Write(f)
			c.Check(err, check.Equals, nil)
			n += _n
		}
		c.Check(buf.Len(), check.Equals, n)
		c.Check(buf.String(), check.Equals, g.gff, check.Commentf("Test: %d", i))
	}
}

func (s *S) TestWriteMetadata(c *check.C) {
	for i, g := range metaTests {
		buf := &bytes.Buffer{}
		w := NewWriter(buf, width, false)
		var n int
		for _, d := range g.write {
			_n, err := w.WriteMetaData(d)
			c.Check(err, check.Equals, nil)
			n += _n
		}
		c.Check(buf.Len(), check.Equals, n)
		c.Check(buf.String(), check.Equals, g.gff, check.Commentf("Test: %d", i))
	}
}