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package fai
import (
"bytes"
"testing"
"github.com/shenwei356/bio/seqio/fastx"
)
func TestFastaReader(t *testing.T) {
file := "seq.fa"
idx, err := New(file)
if err != nil {
t.Errorf("failed to create faidx for %s: %s", file, err)
return
}
// all sequences
seqs, err := fastx.GetSeqs(file, nil, 4, 10, fastx.DefaultIDRegexp)
if err != nil {
t.Errorf("failed to read seqs: %v", err)
}
for _, rec := range seqs {
seq, err := idx.Seq(string(rec.ID))
checkErr(t, err)
if !bytes.Equal(seq, rec.Seq.Seq) {
t.Errorf("unmatched sequences %s: %s", rec.ID, seq)
}
}
//
chr := "cel-let-7"
s, err := idx.Base(chr, 1)
checkErr(t, err)
if s != 'U' {
t.Errorf("unmatched sequences %s: %s", chr, []byte{s})
}
chr = "blank"
seq, err := idx.Seq(chr)
checkErr(t, err)
if string(seq) != "" {
t.Errorf("unmatched sequences %s: %s", chr, seq)
}
chr = "cel-mir-2"
seq, err = idx.Seq(chr)
checkErr(t, err)
if string(seq) != "UAAACAGUAUACAGAAAGCCAUCAAAGC" {
t.Errorf("unmatched sequences %s: %s", chr, seq)
}
start, end := 15, 19
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "AAAGC" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = -3, -1
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "AGC" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 1, -1
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "UAAACAGUAUACAGAAAGCCAUCAAAGC" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 2, -2
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "AAACAGUAUACAGAAAGCCAUCAAAG" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 20, -2
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "CAUCAAAG" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
start, end = 50, -2
seq, err = idx.SubSeq(chr, start, end)
checkErr(t, err)
if string(seq) != "" {
t.Errorf("unmatched sequences %s from %d to %d: %s", chr, start, end, seq)
}
chr = "seq"
seq, err = idx.Seq(chr)
checkErr(t, err)
if string(seq) != "ACTGACTG" {
t.Errorf("unmatched sequences %s: %s", chr, seq)
}
err = idx.Close()
if err != nil {
t.Errorf("fail to close faidx: %v", err)
}
}
func TestFastaReaderNotMapWholeFile(t *testing.T) {
MapWholeFile = false
TestFastaReader(t)
MapWholeFile = true
}
func TestFastaReader2NotMapWholeFile(t *testing.T) {
MapWholeFile = false
TestFastaReader2(t)
MapWholeFile = true
}
func checkErr(t *testing.T, err error) {
if err != nil {
t.Error(err)
}
}
func TestFastaReader2(t *testing.T) {
file := "seq2.fa"
idx, err := New(file)
if err != nil {
t.Errorf("failed to create faidx for %s: %s", file, err)
return
}
seqs, err := fastx.GetSeqs(file, nil, 4, 10, fastx.DefaultIDRegexp)
if err != nil {
t.Errorf("failed to read seqs: %v", err)
}
for _, rec := range seqs {
seq, err := idx.Seq(string(rec.ID))
checkErr(t, err)
if !bytes.Equal(seq, rec.Seq.Seq) {
t.Errorf("unmatched sequences %s: %s", rec.ID, seq)
}
}
err = idx.Close()
if err != nil {
t.Errorf("fail to close faidx: %v", err)
}
}
|
