multi

package
v1.0.1 Latest Latest
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 Go to latest Published: Feb 16, 2017 License: BSD-3-Clause Imports: 13 Imported by: 0

Documentation

Overview

Package multi handles collections of sequences as alignments or sets.

Index

Examples

Constants

This section is empty.

Variables

This section is empty.

Functions

func RegisterJoiner 

func RegisterJoiner(p seq.Sequence, f JoinFunc)

Types

type JoinFunc 

type JoinFunc func(a, b seq.Sequence, where int) (err error)

type Multi 

type Multi struct {
	seq.Annotation
	Seq            []seq.Sequence
	ColumnConsense seq.ConsenseFunc
	Encode         alphabet.Encoding
}

func NewMulti 

func NewMulti(id string, n []seq.Sequence, cons seq.ConsenseFunc) (*Multi, error)

Create a new Multi sequence.

Example 
m, err := NewMulti("example multi",
	[]seq.Sequence{
		linear.NewSeq("example DNA 1", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA),
		linear.NewSeq("example DNA 2", []alphabet.Letter("ACGGTGACCTGGCGCGCAT"), alphabet.DNA),
		linear.NewSeq("example DNA 3", []alphabet.Letter("ACGATGACGTGGCGCTCAT"), alphabet.DNA),
	},
	seq.DefaultConsensus)

if err != nil {
	return
}

fmt.Printf("%- s\n\n%-s\n", m, m.Consensus(false))

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT

acgntgacntggcgcncat

func (*Multi) Add 

func (m *Multi) Add(n ...seq.Sequence) error

Add adds sequences n to the multiple sequence.

Example 
var err error
fmt.Printf("%v %-s\n", m.Rows(), m.Consensus(false))
err = m.Add(linear.NewQSeq("example DNA",
	[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
	alphabet.DNA, alphabet.Sanger))
if err != nil {
	fmt.Println(err)
	return
}
fmt.Printf("%v %-s\n", m.Rows(), m.Consensus(false))
err = m.Add(linear.NewQSeq("example RNA",
	[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
	alphabet.RNA, alphabet.Sanger))
if err != nil {
	fmt.Println(err)
	return
}

Output:

3 acgntgacntggcgcncat
4 acgctgacntggcgcncat
multi: inconsistent alphabets

func (*Multi) Append 

func (m *Multi) Append(i int, a ...alphabet.QLetter) (err error)

Append appends a to the ith sequence in the receiver.

func (*Multi) AppendColumns 

func (m *Multi) AppendColumns(a ...[]alphabet.QLetter) (err error)

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

func (*Multi) AppendEach 

func (m *Multi) AppendEach(a [][]alphabet.QLetter) (err error)

AppendEach appends each []alphabet.QLetter in a to the appropriate sequence in the receiver.

func (*Multi) Clone 

func (m *Multi) Clone() seq.Rower

Clone returns a copy of the sequence.

func (*Multi) Column 

func (m *Multi) Column(pos int, fill bool) []alphabet.Letter

Column returns a slice of letters reflecting the column at pos.

func (*Multi) ColumnQL 

func (m *Multi) ColumnQL(pos int, fill bool) []alphabet.QLetter

ColumnQL returns a slice of quality letters reflecting the column at pos.

func (*Multi) Compose 

func (m *Multi) Compose(fs feat.Set) error

Compose produces a composition of the receiver defined by the features in fs. The result is stored in the receiver and all contributing sequences are modified.

func (*Multi) Conformation 

func (m *Multi) Conformation() feat.Conformation

Conformation returns the sequence conformation.

func (*Multi) Consensus 

func (m *Multi) Consensus(includeMissing bool) *linear.QSeq

Consensus returns a quality sequence reflecting the consensus of the receiver determined by the ColumnConsense field.

func (*Multi) Delete 

func (m *Multi) Delete(i int)

Delete removes the sequence represented at row i of the alignment. It panics if i is out of range.

func (*Multi) Encoding 

func (m *Multi) Encoding() alphabet.Encoding

Encoding returns the quality encoding scheme.

func (*Multi) End 

func (m *Multi) End() int

End returns the end position of the sequence in coordinates relative to the sequence location.

func (*Multi) Flush 

func (m *Multi) Flush(where int, fill alphabet.Letter)

Flush fills ragged sequences with the receiver's gap letter so that all sequences are flush.

func (*Multi) Format 

func (m *Multi) Format(fs fmt.State, c rune)

Format is a support routine for fmt.Formatter. It accepts the formats 'v' and 's' (string), 'a' (fasta) and 'q' (fastq). String, fasta and fastq formats support truncated output via the verb's precision. Fasta format supports sequence line specification via the verb's width field. Fastq format supports optional inclusion of the '+' line descriptor line with the '+' flag. The 'v' verb supports the '#' flag for Go syntax output. The 's' and 'v' formats support the '-' flag for omission of the sequence name and in conjunction with this, the ' ' flag for alignment justification.

func (*Multi) IsFlush 

func (m *Multi) IsFlush(where int) bool

IsFlush returns a boolean indicating whether the end specified by where is flush - that is all the contributing sequences start at the same offset.

Example 
m.Row(3).SetOffset(13)
fmt.Printf("%- s\n\n%-s\n", m, m.Consensus(false))
fmt.Printf("\nFlush at left: %v\nFlush at right: %v\n", m.IsFlush(seq.Start), m.IsFlush(seq.End))
m.Flush(seq.Start, '-')
fmt.Printf("\n%- s\n\n%-s\n", m, m.Consensus(false))
fmt.Printf("\nFlush at left: %v\nFlush at right: %v\n", m.IsFlush(seq.Start), m.IsFlush(seq.End))

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGATGACGTGGCGCTCAT
             acgCtg

acgntgacntggcgcgcat

Flush at left: false
Flush at right: true

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

acgntgacntggcgcgcat

Flush at left: true
Flush at right: true

func (*Multi) Join 

func (m *Multi) Join(a *Multi, where int) error

Join joins a to the receiver at the end specied by where.

Example 
fmt.Printf("%- s\n\n%-s\n", n, n.Consensus(false))
n.Join(m, seq.End)
fmt.Printf("\n%- s\n\n%-s\n", n, n.Consensus(false))

Output:

ACGCTGACTTGGTGCACGT
ACGGTGACCTGGCGCGCAT
ACGtTGACGTGGCGCTCAT
acgCtg

acgctgacntggcgcncat

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

acgctgacntggcgcncatacgntgacntggcgcgcat

func (*Multi) Len 

func (m *Multi) Len() int

Len returns the length of the alignment.

Example 
fmt.Println(m.Len())

Output:

19

func (*Multi) RevComp 

func (m *Multi) RevComp()

RevComp reverse complements the sequence.

Example 
fmt.Printf("%- s\n\n%-s\n\n", m, m.Consensus(false))
m.RevComp()
fmt.Printf("%- s\n\n%-s\n", m, m.Consensus(false))

Output:

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

acgntgacntggcgcgcat

ACGTGCACCAAGTCAGCGT
ATGCGCGCCAGGTCACCGT
ATGAGCGCCACGTCATCGT
caGcgt-------------

atgcgcgccangtcancgt

func (*Multi) Reverse 

func (m *Multi) Reverse()

Reverse reverses the order of letters in the the sequence without complementing them.

func (*Multi) Row 

func (m *Multi) Row(i int) seq.Sequence

Row returns the sequence represented at row i of the alignment. It panics is i is out of range.

func (*Multi) Rows 

func (m *Multi) Rows() int

Rows returns the number of rows in the alignment.

func (*Multi) SetConformation 

func (m *Multi) SetConformation(c feat.Conformation)

SetConformation sets the sequence conformation.

func (*Multi) SetEncoding 

func (m *Multi) SetEncoding(e alphabet.Encoding)

SetEncoding sets the quality encoding scheme to e.

func (*Multi) SetOffset 

func (m *Multi) SetOffset(o int) error

SetOffset sets the location-relative offset of the sequence to o.

func (*Multi) Start 

func (m *Multi) Start() int

Start returns the start position of the sequence in coordinates relative to the sequence location.

func (*Multi) Stitch 

func (m *Multi) Stitch(fs feat.Set) error

Stitch produces a subsequence of the receiver defined by fs. The result is stored in the receiver and all contributing sequences are modified.

Example 
f := fs{
	&fe{s: -1, e: 4},
	&fe{s: 30, e: 38},
}
fmt.Printf("%- s\n\n%-s\n\n", n, n.Consensus(false))
if err := n.Stitch(f); err == nil {
	fmt.Printf("%- s\n\n%-s\n", n, n.Consensus(false))
} else {
	fmt.Println(err)
}

Output:

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

acgctgacntggcgcncatacgntgacntggcgcgcat

ACGCGTGCACGT
ACGGGCGCGCAT
ACGtGCGCTCAT
acgC--acgCtg

acgcgcgcgcat

func (*Multi) String 

func (m *Multi) String() string

func (*Multi) Subseq 

func (m *Multi) Subseq(start, end int) (*Multi, error)

Subseq returns a multiple subsequence slice of the receiver.

func (*Multi) Truncate 

func (m *Multi) Truncate(start, end int) error

Truncate truncates the the receiver from start to end.

Example 
fmt.Printf("%- s\n\n%-s\n\n", m, m.Consensus(false))
m.Truncate(4, 12)
fmt.Printf("%- s\n\n%-s\n", m, m.Consensus(false))

Output:

ACGTGCACCAAGTCAGCGT
ATGCGCGCCAGGTCACCGT
ATGAGCGCCACGTCATCGT
caGcgt-------------

atgcgcgccangtcancgt

GCACCAAG
GCGCCAGG
GCGCCACG
gt------

gcgccang

type Set 

type Set []seq.Sequence

func (Set) AppendEach 

func (s Set) AppendEach(a [][]alphabet.QLetter) (err error)

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

Example 
ss := [][]alphabet.Letter{
	[]alphabet.Letter("ACGCTGACTTGGTGCACGT"),
	[]alphabet.Letter("ACGACTGGGACGT"),
	[]alphabet.Letter("ACGCTGACTGGCCGT"),
	[]alphabet.Letter("GCCTTTGCACGT"),
}
set = make(Set, 4)
for i := range set {
	set[i] = linear.NewSeq(fmt.Sprintf("example DNA %d", i), ss[i], alphabet.DNA)
}
as := [][]alphabet.QLetter{
	alphabet.QLetter{L: 'A'}.Repeat(2),
	alphabet.QLetter{L: 'C'}.Repeat(2),
	alphabet.QLetter{L: 'G'}.Repeat(2),
	alphabet.QLetter{L: 'T'}.Repeat(2),
}

set.AppendEach(as)

for _, s := range set {
	fmt.Printf("%-s\n", s)
}

Output:

ACGCTGACTTGGTGCACGTAA
ACGACTGGGACGTCC
ACGCTGACTGGCCGTGG
GCCTTTGCACGTTT

func (Set) Len 

func (s Set) Len() int
Example 
fmt.Println(set.Len())

Output:

21

func (Set) RevComp 

func (s Set) RevComp()
Example 
set.RevComp()
for _, s := range set {
	fmt.Println(s)
}

Output:

func (Set) Reverse 

func (s Set) Reverse()
Example 
set.RevComp()
for _, s := range set {
	fmt.Println(s)
}

Output:

func (Set) Row 

func (s Set) Row(i int) seq.Sequence

func (Set) Rows 

func (s Set) Rows() (c int)
Example 
fmt.Println(set.Rows())

Output:

4

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