alignment

package
v0.0.0-...-25502c3 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Oct 9, 2012 License: GPL-3.0 Imports: 8 Imported by: 0

Documentation

Overview

Package alignment handles aligned sequences stored as columns.

Index

Examples

Constants

This section is empty.

Variables

This section is empty.

Functions

This section is empty.

Types

type QSeq 

type QSeq struct {
	ID         string
	Desc       string
	Loc        string
	SubIDs     []string
	S          [][]alphabet.QLetter
	Consensify protein.Consensifyer
	Threshold  alphabet.Qphred // Threshold for returning valid letter.
	LowQFilter seq.Filter      // How to represent below threshold letter.
	Stringify  seq.Stringify
	Meta       interface{} // No operation implicitly copies or changes the contents of Meta.
	// contains filtered or unexported fields
}

Aligned protein with quality scores.

func NewQSeq 

func NewQSeq(id string, subids []string, ql [][]alphabet.QLetter, alpha alphabet.Peptide, encode alphabet.Encoding, cons protein.Consensifyer) (*QSeq, error)
Example 
qm, err := NewQSeq("example alignment",
	[]string{"seq 1", "seq 2", "seq 3"},
	[][]alphabet.QLetter{
		{{'A', 40}, {'A', 40}, {'A', 40}},
		{{'C', 40}, {'C', 40}, {'C', 40}},
		{{'G', 40}, {'G', 40}, {'G', 40}},
		{{'C', 40}, {'G', 40}, {'A', 40}},
		{{'T', 40}, {'T', 40}, {'T', 40}},
		{{'G', 40}, {'G', 40}, {'G', 40}},
		{{'A', 40}, {'A', 40}, {'A', 40}},
		{{'C', 40}, {'C', 40}, {'C', 40}},
		{{'T', 40}, {'C', 40}, {'G', 40}},
		{{'T', 40}, {'T', 40}, {'T', 40}},
		{{'G', 40}, {'G', 40}, {'G', 40}},
		{{'G', 40}, {'G', 40}, {'G', 40}},
		{{'T', 40}, {'C', 40}, {'C', 40}},
		{{'G', 40}, {'G', 40}, {'G', 40}},
		{{'C', 40}, {'C', 40}, {'C', 40}},
		{{'A', 40}, {'G', 40}, {'T', 40}},
		{{'C', 40}, {'C', 40}, {'C', 40}},
		{{'G', 40}, {'A', 40}, {'A', 40}},
		{{'T', 40}, {'T', 40}, {'T', 40}},
	},
	alphabet.Protein,
	alphabet.Sanger,
	protein.QConsensify)
if err != nil {
	panic(err)
}

qaligned(qm)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT

acgxtgacxtggcgcxcat

func (*QSeq) Add 

func (self *QSeq) Add(n ...protein.Sequence) (err error)

Add sequences n to Alignment. Sequences in n must align start and end with the receiving alignment. Additional sequence will be clipped.

Example 
fmt.Printf("%v %v\n", qm.Count(), qm)
qm.Add(protein.NewQSeq("example DNA",
	[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
	alphabet.Protein, alphabet.Sanger))
fmt.Printf("%v %v\n", qm.Count(), qm)

Output:

3 acgxtgacxtggcgcxcat
4 acgctgacxtggcgcxcat

func (*QSeq) Alphabet 

func (self *QSeq) Alphabet() alphabet.Alphabet

func (*QSeq) AppendColumns 

func (self *QSeq) AppendColumns(a ...[]alphabet.QLetter) (err error)

Append each byte of each a to the appropriate sequence in the reciever.

func (*QSeq) AppendEach 

func (self *QSeq) AppendEach(a [][]alphabet.QLetter) (err error)

Append each []byte in a to the appropriate sequence in the reciever.

func (*QSeq) At 

func (self *QSeq) At(pos seq.Position) alphabet.QLetter

func (*QSeq) Circular 

func (self *QSeq) Circular(c bool)

func (*QSeq) Column 

func (self *QSeq) Column(pos int, _ bool) (c []alphabet.Letter)

func (*QSeq) ColumnQL 

func (self *QSeq) ColumnQL(pos int, _ bool) []alphabet.QLetter

func (*QSeq) Compose 

func (self *QSeq) Compose(f feat.FeatureSet) (err error)

func (*QSeq) Consensus 

func (self *QSeq) Consensus(_ bool) (qs *protein.QSeq)

func (*QSeq) Copy 

func (self *QSeq) Copy() seq.Sequence
Example 
qn = qm.Copy().(*QSeq)
qn.Set(seq.Position{Pos: 3, Ind: 2}, alphabet.QLetter{L: 't', Q: 40})
qaligned(qm)
fmt.Println()
qaligned(qn)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

func (*QSeq) Count 

func (self *QSeq) Count() int
Example 
fmt.Println(qm.Count())

Output:

4

func (*QSeq) Description 

func (self *QSeq) Description() *string

Description returns a pointer to the Desc string of the sequence.

func (*QSeq) EAt 

func (self *QSeq) EAt(pos seq.Position) float64

func (*QSeq) Encoding 

func (self *QSeq) Encoding() alphabet.Encoding

func (*QSeq) End 

func (self *QSeq) End() int

func (*QSeq) Extract 

func (self *QSeq) Extract(i int) protein.Sequence

func (*QSeq) IsCircular 

func (self *QSeq) IsCircular() bool

func (*QSeq) Join 

func (self *QSeq) Join(p *QSeq, where int) (err error)
Example 
qaligned(qn)
qn.Join(qm, seq.End)
fmt.Println()
qaligned(qn)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

ACGCTGACTTGGTGCACGTACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCATACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCATACGATGACGTGGCGCTCAT
acgCtg-------------acgCtg-------------

acgctgacxtggcgcxcatacgctgacxtggcgcxcat

func (*QSeq) Len 

func (self *QSeq) Len() int

func (*QSeq) Location 

func (self *QSeq) Location() *string

Location returns a pointer to the Loc string of the sequence.

func (*QSeq) Name 

func (self *QSeq) Name() *string

Name returns a pointer to the ID string of the sequence.

func (*QSeq) Offset 

func (self *QSeq) Offset(o int)

func (*QSeq) Protein 

func (self *QSeq) Protein()

Required to satisfy protein.Sequence interface.

func (*QSeq) QDecode 

func (self *QSeq) QDecode(l byte) alphabet.Qphred

func (*QSeq) QEncode 

func (self *QSeq) QEncode(pos seq.Position) byte

func (*QSeq) Raw 

func (self *QSeq) Raw() interface{}

Raw returns a pointer to the underlying [][]alphabet.QLetter slice.

func (*QSeq) Reverse 

func (self *QSeq) Reverse()
Example 
qaligned(qm)
fmt.Println()
qm.Reverse()
qaligned(qm)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

TGCACGTGGTTCAGTCGCA
TACGCGCGGTCCAGTGGCA
TACTCGCGGTGCAGTAGCA
-------------gtCgca

tacxcgcggtxcagtcgca

func (*QSeq) Set 

func (self *QSeq) Set(pos seq.Position, l alphabet.QLetter)

func (*QSeq) SetE 

func (self *QSeq) SetE(pos seq.Position, l float64)

func (*QSeq) SetEncoding 

func (self *QSeq) SetEncoding(e alphabet.Encoding)

Set the quality encoding type to e.

func (*QSeq) Start 

func (self *QSeq) Start() int

func (*QSeq) Stitch 

func (self *QSeq) Stitch(f feat.FeatureSet) (err error)
Example 
f := feat.FeatureSet{
	&feat.Feature{Start: -1, End: 4},
	&feat.Feature{Start: 30, End: 38},
}
qaligned(qn)
fmt.Println()
err := qn.Stitch(f)
if err != nil {
	fmt.Println(err)
} else {
	qaligned(qn)
}

Output:

ACGCTGACTTGGTGCACGTACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCATACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCATACGATGACGTGGCGCTCAT
acgCtg-------------acgCtg-------------

acgctgacxtggcgcxcatacgctgacxtggcgcxcat

ACGCGTGCACGT
ACGGGCGCGCAT
ACGtGCGCTCAT
acgC--------

acgcgcgcxcat

func (*QSeq) String 

func (self *QSeq) String() string

func (*QSeq) Subseq 

func (self *QSeq) Subseq(start int, end int) (sub seq.Sequence, err error)

Return a subsequence from start to end, wrapping if the sequence is circular.

func (*QSeq) Truncate 

func (self *QSeq) Truncate(start int, end int) (err error)
Example 
qaligned(qm)
qm.Truncate(4, 12)
fmt.Println()
qaligned(qm)

Output:

TGCACGTGGTTCAGTCGCA
TACGCGCGGTCCAGTGGCA
TACTCGCGGTGCAGTAGCA
-------------gtCgca

tacxcgcggtxcagtcgca

CGTGGTTC
CGCGGTCC
CGCGGTGC
--------

cgcggtxc

type Seq 

type Seq struct {
	ID         string
	Desc       string
	Loc        string
	SubIDs     []string
	S          [][]alphabet.Letter
	Consensify protein.Consensifyer
	Stringify  seq.Stringify
	Meta       interface{} // No operation implicitly copies or changes the contents of Meta.
	// contains filtered or unexported fields
}

Alignment protein sequence.

func NewSeq 

func NewSeq(id string, subids []string, b [][]alphabet.Letter, alpha alphabet.Peptide, cons protein.Consensifyer) (*Seq, error)
Example 
m, err := NewSeq("example alignment",
	[]string{"seq 1", "seq 2", "seq 3"},
	[][]alphabet.Letter{
		[]alphabet.Letter("AAA"),
		[]alphabet.Letter("CCC"),
		[]alphabet.Letter("GGG"),
		[]alphabet.Letter("CGA"),
		[]alphabet.Letter("TTT"),
		[]alphabet.Letter("GGG"),
		[]alphabet.Letter("AAA"),
		[]alphabet.Letter("CCC"),
		[]alphabet.Letter("TCG"),
		[]alphabet.Letter("TTT"),
		[]alphabet.Letter("GGG"),
		[]alphabet.Letter("GGG"),
		[]alphabet.Letter("TCC"),
		[]alphabet.Letter("GGG"),
		[]alphabet.Letter("CCC"),
		[]alphabet.Letter("AGT"),
		[]alphabet.Letter("CCC"),
		[]alphabet.Letter("GAA"),
		[]alphabet.Letter("TTT"),
	},
	alphabet.Protein,
	protein.Consensify)
if err != nil {
	panic(err)
}

aligned(m)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT

acgxtgacxtggcgcxcat

func (*Seq) Add 

func (self *Seq) Add(n ...protein.Sequence) (err error)

Add sequences n to Seq. Sequences in n must align start and end with the receiving alignment. Additional sequence will be clipped.

Example 
fmt.Printf("%v %v\n", m.Count(), m)
m.Add(protein.NewQSeq("example Protein",
	[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
	alphabet.Protein, alphabet.Sanger))
fmt.Printf("%v %v\n", m.Count(), m)

Output:

3 acgxtgacxtggcgcxcat
4 acgctgacxtggcgcxcat

func (*Seq) Alphabet 

func (self *Seq) Alphabet() alphabet.Alphabet

func (*Seq) AppendColumns 

func (self *Seq) AppendColumns(a ...[]alphabet.QLetter) (err error)

Append each byte of each a to the appropriate sequence in the reciever.

func (*Seq) AppendEach 

func (self *Seq) AppendEach(a [][]alphabet.QLetter) (err error)

Append each []byte in a to the appropriate sequence in the reciever.

func (*Seq) At 

func (self *Seq) At(pos seq.Position) alphabet.QLetter

func (*Seq) Circular 

func (self *Seq) Circular(c bool)

func (*Seq) Column 

func (self *Seq) Column(pos int, _ bool) (c []alphabet.Letter)

func (*Seq) ColumnQL 

func (self *Seq) ColumnQL(pos int, _ bool) (c []alphabet.QLetter)

func (*Seq) Compose 

func (self *Seq) Compose(f feat.FeatureSet) (err error)

func (*Seq) Consensus 

func (self *Seq) Consensus(_ bool) (qs *protein.QSeq)

func (*Seq) Copy 

func (self *Seq) Copy() seq.Sequence
Example 
n = m.Copy().(*Seq)
n.Set(seq.Position{Pos: 3, Ind: 2}, alphabet.QLetter{L: 't'})
aligned(m)
fmt.Println()
aligned(n)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

func (*Seq) Count 

func (self *Seq) Count() int
Example 
fmt.Println(m.Count())

Output:

4

func (*Seq) Description 

func (self *Seq) Description() *string

Description returns a pointer to the Desc string of the sequence.

func (*Seq) End 

func (self *Seq) End() int

func (*Seq) Extract 

func (self *Seq) Extract(i int) protein.Sequence

func (*Seq) IsCircular 

func (self *Seq) IsCircular() bool

func (*Seq) Join 

func (self *Seq) Join(p *Seq, where int) (err error)
Example 
aligned(n)
n.Join(m, seq.End)
fmt.Println()
aligned(n)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

ACGCTGACTTGGTGCACGTACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCATACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCATACGATGACGTGGCGCTCAT
acgCtg-------------acgCtg-------------

acgctgacxtggcgcxcatacgctgacxtggcgcxcat

func (*Seq) Len 

func (self *Seq) Len() int

func (*Seq) Location 

func (self *Seq) Location() *string

Location returns a pointer to the Loc string of the sequence.

func (*Seq) Name 

func (self *Seq) Name() *string

Name returns a pointer to the ID string of the sequence.

func (*Seq) Offset 

func (self *Seq) Offset(o int)

func (*Seq) Protein 

func (self *Seq) Protein()

Required to satisfy protein.Sequence interface.

func (*Seq) Raw 

func (self *Seq) Raw() interface{}

Raw returns a pointer to the underlying [][]byte slice.

func (*Seq) Reverse 

func (self *Seq) Reverse()
Example 
aligned(m)
fmt.Println()
m.Reverse()
aligned(m)

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT
acgCtg-------------

acgctgacxtggcgcxcat

TGCACGTGGTTCAGTCGCA
TACGCGCGGTCCAGTGGCA
TACTCGCGGTGCAGTAGCA
-------------gtCgca

tacxcgcggtxcagtcgca

func (*Seq) Set 

func (self *Seq) Set(pos seq.Position, l alphabet.QLetter)

func (*Seq) Start 

func (self *Seq) Start() int

func (*Seq) Stitch 

func (self *Seq) Stitch(f feat.FeatureSet) (err error)
Example 
f := feat.FeatureSet{
	&feat.Feature{Start: -1, End: 4},
	&feat.Feature{Start: 30, End: 38},
}
aligned(n)
fmt.Println()
err := n.Stitch(f)
if err != nil {
	fmt.Println(err)
} else {
	aligned(n)
}

Output:

ACGCTGACTTGGTGCACGTACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCATACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCATACGATGACGTGGCGCTCAT
acgCtg-------------acgCtg-------------

acgctgacxtggcgcxcatacgctgacxtggcgcxcat

ACGCGTGCACGT
ACGGGCGCGCAT
ACGtGCGCTCAT
acgC--------

acgcgcgcxcat

func (*Seq) String 

func (self *Seq) String() string

func (*Seq) Subseq 

func (self *Seq) Subseq(start int, end int) (sub seq.Sequence, err error)

Return a subsequence from start to end, wrapping if the sequence is circular.

func (*Seq) Truncate 

func (self *Seq) Truncate(start int, end int) (err error)
Example 
aligned(m)
m.Truncate(4, 12)
fmt.Println()
aligned(m)

Output:

TGCACGTGGTTCAGTCGCA
TACGCGCGGTCCAGTGGCA
TACTCGCGGTGCAGTAGCA
-------------gtCgca

tacxcgcggtxcagtcgca

CGTGGTTC
CGCGGTCC
CGCGGTGC
--------

cgcggtxc

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.