1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
|
package fastx
import (
"fmt"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/util/byteutil"
"github.com/shenwei356/xopen"
)
// Record is a struct for FASTA/Q
type Record struct {
ID []byte // id
Name []byte // full name
Desc []byte // Description
Seq *seq.Seq // seq
}
// Clone of a Record
func (record *Record) Clone() *Record {
return &Record{
[]byte(string(record.ID)),
[]byte(string(record.Name)),
[]byte(string(record.Desc)),
record.Seq.Clone(),
}
}
func (record *Record) String() string {
return string(record.Format(60))
}
// NewRecord is constructor of type Record for FASTA
func NewRecord(t *seq.Alphabet, id, name, desc, s []byte) (*Record, error) {
seq, err := seq.NewSeq(t, s)
if err != nil {
return nil, fmt.Errorf("error when parsing seq: %s (%s)", id, err)
}
return &Record{id, name, desc, seq}, nil
}
// NewRecordWithoutValidation is constructor of type Record for FASTA
// without validation of the sequence
func NewRecordWithoutValidation(t *seq.Alphabet, id, name, desc, s []byte) (*Record, error) {
seq, err := seq.NewSeqWithoutValidation(t, s)
if err != nil {
return nil, err
}
return &Record{id, name, desc, seq}, nil
}
// NewRecordWithSeq is constructor of type Record
// for FASTA with a existed seq.Seq object
func NewRecordWithSeq(id, name, desc []byte, s *seq.Seq) (*Record, error) {
return &Record{id, name, desc, s}, nil
}
// NewRecordWithQual is constructor of type Record for FASTQ
func NewRecordWithQual(t *seq.Alphabet, id, name, desc, s, q []byte) (*Record, error) {
seq, err := seq.NewSeqWithQual(t, s, q)
if err != nil {
return nil, fmt.Errorf("error when parsing seq: %s (%s)", id, err)
}
return &Record{id, name, desc, seq}, nil
}
// NewRecordWithQualWithoutValidation is constructor of type Record for FASTQ
func NewRecordWithQualWithoutValidation(t *seq.Alphabet, id, name, desc, s, q []byte) (*Record, error) {
seq, err := seq.NewSeqWithQualWithoutValidation(t, s, q)
if err != nil {
return nil, err
}
return &Record{id, name, desc, seq}, nil
}
// ForcelyOutputFastq means outputing record as fastq even if it has no quality (zero-length fastq)
var ForcelyOutputFastq bool
// Format returns formated (wrapped with fixed length of) sequence record
func (record *Record) Format(width int) []byte {
if len(record.Seq.Qual) > 0 || ForcelyOutputFastq {
return append(append(append(append([]byte(fmt.Sprintf("@%s\n", record.Name)),
byteutil.WrapByteSlice(record.Seq.Seq, width)...), []byte("\n+\n")...),
byteutil.WrapByteSlice(record.Seq.Qual, width)...), []byte("\n")...)
}
return append(append([]byte(fmt.Sprintf(">%s\n", record.Name)),
byteutil.WrapByteSlice(record.Seq.Seq, width)...), []byte("\n")...)
}
var defaultBytesBufferSize = 1 << 20
// bufferedByteSliceWrapper is for function FormatToWriter
var bufferedByteSliceWrapper *byteutil.BufferedByteSliceWrapper
func init() {
bufferedByteSliceWrapper = byteutil.NewBufferedByteSliceWrapper(1, defaultBytesBufferSize)
}
// FormatToWriter formats and directly writes to writer
func (record *Record) FormatToWriter(outfh *xopen.Writer, width int) {
if len(record.Seq.Qual) > 0 || ForcelyOutputFastq {
outfh.Write([]byte(fmt.Sprintf("@%s\n", record.Name)))
if len(record.Seq.Seq) <= pageSize {
outfh.Write(byteutil.WrapByteSlice(record.Seq.Seq, width))
} else {
text, b := bufferedByteSliceWrapper.Wrap(record.Seq.Seq, width)
outfh.Write(text)
outfh.Flush()
bufferedByteSliceWrapper.Recycle(b)
}
outfh.Write([]byte("\n+\n"))
if len(record.Seq.Qual) <= pageSize {
outfh.Write(byteutil.WrapByteSlice(record.Seq.Qual, width))
} else {
text, b := bufferedByteSliceWrapper.Wrap(record.Seq.Qual, width)
outfh.Write(text)
outfh.Flush()
bufferedByteSliceWrapper.Recycle(b)
}
outfh.Write([]byte("\n"))
return
}
outfh.Write([]byte(fmt.Sprintf(">%s\n", record.Name)))
if len(record.Seq.Seq) <= pageSize {
outfh.Write(byteutil.WrapByteSlice(record.Seq.Seq, width))
} else {
text, b := bufferedByteSliceWrapper.Wrap(record.Seq.Seq, width)
outfh.Write(text)
outfh.Flush()
bufferedByteSliceWrapper.Recycle(b)
}
outfh.Write([]byte("\n"))
}
|
