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|
// Copyright ©2013 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 fai
import (
"bytes"
"encoding/csv"
"errors"
"reflect"
"strconv"
"strings"
"testing"
)
func TestNewIndex(t *testing.T) {
for i, test := range []struct {
in string
idx Index
err error
}{
{
in: ``,
idx: Index{},
err: nil,
},
{
in: `>FN654386.1
TTTTTCAAAGACGTTAAGAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAAAACGAGATTC
TCGTGTTGCTTCTCGGTCATACCAAAGACC
>FN654386.2
GCGAACTGATGGTCAAGCACAGCTAGAACGTCTTCGTTTGAAGCTGGAGACGATTGCCGCGCAGGCAACT
CGCCGACATCGACGATGTCTTCGTAGTCAT
>FN654386.3
CTGAATTGAGCCGCGGGCGATTGATTCGTGTCGGCGCGTCAGGAGGAAGTTCAAGTCGGAATCTCGCGTT
TTCATTAATCATTTGTACTGGATCTGTTCG
`,
// Index validated against samtools faidx for this set of sequences.
idx: Index{
"FN654386.1": Record{Name: "FN654386.1", Length: 100, Start: 12, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.2": Record{Name: "FN654386.2", Length: 100, Start: 126, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.3": Record{Name: "FN654386.3", Length: 100, Start: 240, BasesPerLine: 70, BytesPerLine: 71},
},
err: nil,
},
{
// Index validated against samtools faidx for this set of sequences.
in: `>FN654386.1 descriptive text separated by tab
TTTTTCAAAGACGTTAAGAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAAAACGAGATTC
TCGTGTTGCTTCTCGGTCATACCAAAGACC
>FN654386.2 descriptive text separated by space
GCGAACTGATGGTCAAGCACAGCTAGAACGTCTTCGTTTGAAGCTGGAGACGATTGCCGCGCAGGCAACT
CGCCGACATCGACGATGTCTTCGTAGTCAT
>FN654386.3
CTGAATTGAGCCGCGGGCGATTGATTCGTGTCGGCGCGTCAGGAGGAAGTTCAAGTCGGAATCTCGCGTT
TTCATTAATCATTTGTACTGGATCTGTTCG
`,
// Index validated against samtools faidx for this set of sequences.
idx: Index{
"FN654386.1": Record{Name: "FN654386.1", Length: 100, Start: 46, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.2": Record{Name: "FN654386.2", Length: 100, Start: 196, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.3": Record{Name: "FN654386.3", Length: 100, Start: 310, BasesPerLine: 70, BytesPerLine: 71},
},
err: nil,
},
{
in: `>FN654386.1
TTTTTCAAAGACGTTAAGAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAA
TCGTGTTGCTTCTCGGTCATACCAAAGACC
>FN654386.2
GCGAACTGATGGTCAAGCACAGCTAGAACGTCTTCGTTTGAAGCTGGAGACGATTGCCGCGCAGGCAACT
CGCCGACATCGACGATGTCTTCGTAGTCAT
>FN654386.3
CTGAATTGAGCCGCGGGCGATTGATTCGTGTCGGCGCGTCAGGAGGAAGTTCAAGTCGGAATCTCGCGTT
TTCATTAATCATTTGTACTGGATCTGTTCG
`,
// Index validated against samtools faidx for this set of sequences.
idx: Index{
"FN654386.1": Record{Name: "FN654386.1", Length: 90, Start: 12, BasesPerLine: 60, BytesPerLine: 61},
"FN654386.2": Record{Name: "FN654386.2", Length: 100, Start: 116, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.3": Record{Name: "FN654386.3", Length: 100, Start: 230, BasesPerLine: 70, BytesPerLine: 71},
},
err: nil,
},
{
in: `>FN654386.1
TTTTTCAAAGACGTTAAGAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAAAACGAGATTC
TCGTGTTGCTTCTCGGTCATACCAAAGACC
>FN654386.1
GCGAACTGATGGTCAAGCACAGCTAGAACGTCTTCGTTTGAAGCTGGAGACGATTGCCGCGCAGGCAACT
CGCCGACATCGACGATGTCTTCGTAGTCAT
>FN654386.3
CTGAATTGAGCCGCGGGCGATTGATTCGTGTCGGCGCGTCAGGAGGAAGTTCAAGTCGGAATCTCGCGTT
TTCATTAATCATTTGTACTGGATCTGTTCG
`,
idx: nil,
err: errors.New("fai: duplicate sequence identifier FN654386.1 at 114"),
},
{
in: `>FN654386.1
TTTTTCAAAGACGTTAAGAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAAAACGAGATTC
GAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAAAACGAGATTCTTTTTCAAAGACGTTA
TCGTGTTGCTTCTCGGTCATACCAAAGACC
>FN654386.2
GCGAACTGATGGTCAAGCACAGCTAGAACGTCTTCGTTTGAAGCTGGAGACGATTGCCGCGCAGGCAACT
CGCCGACATCGACGATGTCTTCGTAGTCAT
>FN654386.3
CTGAATTGAGCCGCGGGCGATTGATTCGTGTCGGCGCGTCAGGAGGAAGTTCAAGTCGGAATCTCGCGTT
TTCATTAATCATTTGTACTGGATCTGTTCG
`,
idx: nil,
err: errors.New("fai: unexpected short line before offset 153"),
},
{
in: `>FN654386.1
TTTTTCAAAGACGTTAAGAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAAAACGAGATTC
GAGCATCAAACAGAATCATTTTGTTCTCGGATGAGAAGCTGAAAACGAGATTCTTTTTCAAAGACGTTACG
TCGTGTTGCTTCTCGGTCATACCAAAGACC
>FN654386.2
GCGAACTGATGGTCAAGCACAGCTAGAACGTCTTCGTTTGAAGCTGGAGACGATTGCCGCGCAGGCAACT
CGCCGACATCGACGATGTCTTCGTAGTCAT
>FN654386.3
CTGAATTGAGCCGCGGGCGATTGATTCGTGTCGGCGCGTCAGGAGGAAGTTCAAGTCGGAATCTCGCGTT
TTCATTAATCATTTGTACTGGATCTGTTCG
`,
idx: nil,
err: errors.New("fai: unexpected long line at offset 83"),
},
} {
got, err := NewIndex(strings.NewReader(test.in))
if !reflect.DeepEqual(err, test.err) {
t.Errorf("unexpected error: got:%v want:%v", err, test.err)
}
if !reflect.DeepEqual(got, test.idx) {
t.Errorf("unexpected result for test %d: got:%#v want:%#v", i, got, test.idx)
}
}
}
func TestReadFrom(t *testing.T) {
for i, test := range []struct {
in string
idx Index
err error
}{
{
in: ``,
idx: nil,
err: nil,
},
{
in: `NODE_7194_length_226_cov_2.672566 246 35 60 61
NODE_7195_length_193_cov_2.906736 213 321 60 61
NODE_7419_length_181_cov_4.668508 201 573 60 61
NODE_7473_length_222_cov_10.977477 242 814 60 61
NODE_11804_length_273_cov_2.186813 293 1097 60 61
NODE_12878_length_198_cov_2.358586 218 1431 60 61
NODE_19170_length_305_cov_2.147541 325 1689 60 61
NODE_23972_length_201_cov_2.452736 221 2056 60 61
NODE_25171_length_223_cov_2.869955 243 2317 60 61
NODE_26170_length_196_cov_2.658163 216 2601 60 61
NODE_28488_length_231_cov_2.290043 251 2857 60 61
NODE_29471_length_195_cov_5.102564 215 3149 60 61
NODE_30404_length_252_cov_1.480159 272 3404 60 61
NODE_30635_length_192_cov_2.947917 212 3717 60 61
NODE_34404_length_184_cov_7.989130 204 3969 60 61
NODE_36516_length_195_cov_3.517949 215 4213 60 61
NODE_41230_length_277_cov_3.498195 297 4468 60 61
NODE_42422_length_182_cov_2.609890 202 4806 60 61
NODE_43724_length_236_cov_3.500000 256 5048 60 61
NODE_44676_length_185_cov_1.421622 205 5345 60 61
NODE_53327_length_192_cov_1.854167 212 5590 60 61
`,
idx: Index{
"NODE_7194_length_226_cov_2.672566": Record{Name: "NODE_7194_length_226_cov_2.672566", Length: 246, Start: 35, BasesPerLine: 60, BytesPerLine: 61},
"NODE_7195_length_193_cov_2.906736": Record{Name: "NODE_7195_length_193_cov_2.906736", Length: 213, Start: 321, BasesPerLine: 60, BytesPerLine: 61},
"NODE_7419_length_181_cov_4.668508": Record{Name: "NODE_7419_length_181_cov_4.668508", Length: 201, Start: 573, BasesPerLine: 60, BytesPerLine: 61},
"NODE_7473_length_222_cov_10.977477": Record{Name: "NODE_7473_length_222_cov_10.977477", Length: 242, Start: 814, BasesPerLine: 60, BytesPerLine: 61},
"NODE_11804_length_273_cov_2.186813": Record{Name: "NODE_11804_length_273_cov_2.186813", Length: 293, Start: 1097, BasesPerLine: 60, BytesPerLine: 61},
"NODE_12878_length_198_cov_2.358586": Record{Name: "NODE_12878_length_198_cov_2.358586", Length: 218, Start: 1431, BasesPerLine: 60, BytesPerLine: 61},
"NODE_19170_length_305_cov_2.147541": Record{Name: "NODE_19170_length_305_cov_2.147541", Length: 325, Start: 1689, BasesPerLine: 60, BytesPerLine: 61},
"NODE_23972_length_201_cov_2.452736": Record{Name: "NODE_23972_length_201_cov_2.452736", Length: 221, Start: 2056, BasesPerLine: 60, BytesPerLine: 61},
"NODE_25171_length_223_cov_2.869955": Record{Name: "NODE_25171_length_223_cov_2.869955", Length: 243, Start: 2317, BasesPerLine: 60, BytesPerLine: 61},
"NODE_26170_length_196_cov_2.658163": Record{Name: "NODE_26170_length_196_cov_2.658163", Length: 216, Start: 2601, BasesPerLine: 60, BytesPerLine: 61},
"NODE_28488_length_231_cov_2.290043": Record{Name: "NODE_28488_length_231_cov_2.290043", Length: 251, Start: 2857, BasesPerLine: 60, BytesPerLine: 61},
"NODE_29471_length_195_cov_5.102564": Record{Name: "NODE_29471_length_195_cov_5.102564", Length: 215, Start: 3149, BasesPerLine: 60, BytesPerLine: 61},
"NODE_30404_length_252_cov_1.480159": Record{Name: "NODE_30404_length_252_cov_1.480159", Length: 272, Start: 3404, BasesPerLine: 60, BytesPerLine: 61},
"NODE_30635_length_192_cov_2.947917": Record{Name: "NODE_30635_length_192_cov_2.947917", Length: 212, Start: 3717, BasesPerLine: 60, BytesPerLine: 61},
"NODE_34404_length_184_cov_7.989130": Record{Name: "NODE_34404_length_184_cov_7.989130", Length: 204, Start: 3969, BasesPerLine: 60, BytesPerLine: 61},
"NODE_36516_length_195_cov_3.517949": Record{Name: "NODE_36516_length_195_cov_3.517949", Length: 215, Start: 4213, BasesPerLine: 60, BytesPerLine: 61},
"NODE_41230_length_277_cov_3.498195": Record{Name: "NODE_41230_length_277_cov_3.498195", Length: 297, Start: 4468, BasesPerLine: 60, BytesPerLine: 61},
"NODE_42422_length_182_cov_2.609890": Record{Name: "NODE_42422_length_182_cov_2.609890", Length: 202, Start: 4806, BasesPerLine: 60, BytesPerLine: 61},
"NODE_43724_length_236_cov_3.500000": Record{Name: "NODE_43724_length_236_cov_3.500000", Length: 256, Start: 5048, BasesPerLine: 60, BytesPerLine: 61},
"NODE_44676_length_185_cov_1.421622": Record{Name: "NODE_44676_length_185_cov_1.421622", Length: 205, Start: 5345, BasesPerLine: 60, BytesPerLine: 61},
"NODE_53327_length_192_cov_1.854167": Record{Name: "NODE_53327_length_192_cov_1.854167", Length: 212, Start: 5590, BasesPerLine: 60, BytesPerLine: 61},
},
err: nil,
},
{
in: `NODE_7194_length_226_cov_2.672566 246 35 60 61
NODE_7195_length_193_cov_2.906736 213 321 60 61
NODE_7419_length_181_cov_4.668508 201 573 60 61
NODE_7473_length_222_cov_10.977477 242 814 60 61
NODE_11804_length_273_cov_2.186813 293 1097 60 61
NODE_12878_length_198_cov_2.358586 218 1431 60 61
NODE_19170_length_305_cov_2.147541 325 1689 60 61
NODE_23972_length_201_cov_2`,
idx: nil,
err: parseError(8, 1, csv.ErrFieldCount),
},
{
in: `NODE_7194_length_226_cov_2.672566 246 35 60 61
NODE_7195_length_193_cov_2.906736 213 321 60 61
NODE_7419_length_181_cov_4.668508 201 573 60 61
NODE_7473_length_222_cov_10.977477 242 814 60 61
NODE_11804_length_273_cov_2.186813 293 1097 60 61
NODE_12878_length_198_cov_2.358586 218 1431 60 61
NODE_19170_length_305_cov_2.147541 325 1689 60 61
NODE_23972_length_201_cov_2.452736 221 2056 60 61
NODE_25171_length_223_cov_2.869955 243 2317 60 61
NODE_26170_length_196_cov_2.658163 216 2601 60 61
NODE_28488_length_231_cov_2.290043 251 2857 60 61
NODE_29471_length_195_cov_5.102564 215 3149 60 61
NODE_30404_length_252_cov_1.480159 272 3404 60 61` + "\t" + `
NODE_30635_length_192_cov_2.947917 212 3717 60 61
NODE_34404_length_184_cov_7.989130 204 3969 60 61
NODE_36516_length_195_cov_3.517949 215 4213 60 61
NODE_41230_length_277_cov_3.498195 297 4468 60 61
NODE_42422_length_182_cov_2.609890 202 4806 60 61
NODE_43724_length_236_cov_3.500000 256 5048 60 61
NODE_44676_length_185_cov_1.421622 205 5345 60 61
NODE_53327_length_192_cov_1.854167 212 5590 60 61
`,
idx: nil,
err: parseError(13, 1, csv.ErrFieldCount),
},
{
in: `NODE_7194_length_226_cov_2.672566 246 35 60 61
NODE_7195_length_193_cov_2.906736 213 321 60 61
NODE_7419_length_181_cov_4.668508 201 573 60 61
NODE_7473_length_222_cov_10.977477 242 814 60 61
NODE_11804_length_273_cov_2.186813 293 1097 60 61
NODE_12878_length_198_cov_2.358586 218 1431 60 61
NODE_19170_length_305_cov_2.147541 325 1689 60 61
NODE_23972_length_201_cov_2.452736 221 2056 60 61
NODE_25171_length_223_cov_2.869955 243 2317 60 61
NODE_26170_length_196_cov_2.658163 216 2601 60 61
NODE_28488_length_231_cov_2.290043 251 2857 60 61
NODE_29471_length_195_cov_5.102564 215 3149 60 61
NODE_30404_length_252_cov_1.480159 272 3404 60 61
NODE_12878_length_198_cov_2.358586 218 1431 60 61
NODE_34404_length_184_cov_7.989130 204 3969 60 61
NODE_36516_length_195_cov_3.517949 215 4213 60 61
NODE_41230_length_277_cov_3.498195 297 4468 60 61
NODE_42422_length_182_cov_2.609890 202 4806 60 61
NODE_43724_length_236_cov_3.500000 256 5048 60 61
NODE_44676_length_185_cov_1.421622 205 5345 60 61
NODE_53327_length_192_cov_1.854167 212 5590 60 61
`,
idx: nil,
err: parseError(14, 0, ErrNonUnique),
},
{
in: `NODE_7194_length_226_cov_2.672566 246 35 60 61
NODE_7195_length_193_cov_2.906736 213 321 60 61
NODE_7419_length_181_cov_4.668508 201 573 60 61
NODE_7473_length_222_cov_10.977477 242 814 60 61
NODE_11804_length_273_cov_2.186813 293 1097 60 61
NODE_12878_length_198_cov_2.358586 218 1431 60 61
NODE_19170_length_305_cov_2.147541 325 1689 60 61
NODE_23972_length_201_cov_2.452736 221 2056 sixty 61
NODE_25171_length_223_cov_2.869955 243 2317 60 61
NODE_26170_length_196_cov_2.658163 216 2601 60 61
NODE_28488_length_231_cov_2.290043 251 2857 60 61
NODE_29471_length_195_cov_5.102564 215 3149 60 61
NODE_30404_length_252_cov_1.480159 272 3404 60 61
NODE_30635_length_192_cov_2.947917 212 3717 60 61
NODE_34404_length_184_cov_7.989130 204 3969 60 61
NODE_36516_length_195_cov_3.517949 215 4213 60 61
NODE_41230_length_277_cov_3.498195 297 4468 60 61
NODE_42422_length_182_cov_2.609890 202 4806 60 61
NODE_43724_length_236_cov_3.500000 256 5048 60 61
NODE_44676_length_185_cov_1.421622 205 5345 60 61
NODE_53327_length_192_cov_1.854167 212 5590 60 61
`,
idx: nil,
err: parseError(8, 3, &strconv.NumError{"ParseInt", "sixty", strconv.ErrSyntax}),
},
} {
got, err := ReadFrom(strings.NewReader(test.in))
if !reflect.DeepEqual(err, dropCSVColumn(test.err)) {
t.Errorf("unexpected error for test %d: got:%#v want:%#v", i, err, test.err)
}
if !reflect.DeepEqual(got, test.idx) {
t.Errorf("unexpected result for test %d: got:%#v want:%#v", i, got, test.idx)
}
}
}
func TestWriteTo(t *testing.T) {
for i, test := range []struct {
idx Index
want string
}{
{
idx: Index{
"FN654386.1": Record{Name: "FN654386.1", Length: 100, Start: 12, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.2": Record{Name: "FN654386.2", Length: 100, Start: 126, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.3": Record{Name: "FN654386.3", Length: 100, Start: 240, BasesPerLine: 70, BytesPerLine: 71},
},
want: `FN654386.1 100 12 70 71
FN654386.2 100 126 70 71
FN654386.3 100 240 70 71
`,
},
{
// Map iteration order is stated to be unspecified, but in practice,
// maps that are shorter than one bucket have consistent order, so
// provide a different ordering.
idx: Index{
"FN654386.2": Record{Name: "FN654386.2", Length: 100, Start: 126, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.1": Record{Name: "FN654386.1", Length: 100, Start: 12, BasesPerLine: 70, BytesPerLine: 71},
"FN654386.3": Record{Name: "FN654386.3", Length: 100, Start: 240, BasesPerLine: 70, BytesPerLine: 71},
},
want: `FN654386.1 100 12 70 71
FN654386.2 100 126 70 71
FN654386.3 100 240 70 71
`,
},
} {
var buf bytes.Buffer
err := WriteTo(&buf, test.idx)
if err != nil {
t.Errorf("unexpected error: got:%v", err)
}
got := buf.String()
if got != test.want {
t.Errorf("unexpected result for test %d: got:\n%s\nwant:%s", i, got, test.want)
}
}
}
|
