Documentation
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Index ¶
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
func SeqColToDense ¶
func SeqColToDense(sc SequenceCollection) *Dense
func TruncatedSVD ¶
func TruncatedSVD(data Matrix, k int) *Dense
Types ¶
type ReducedSequence ¶
type ReducedSequence struct {
Header string //contig id from fasta file
Hist []float64 // Un-normalized LBP histogram
Svd []float64 // SVD reduced dimension vector
Kmers string
}
func NewReducedSequence ¶
func NewReducedSequence() *ReducedSequence
type Sequence ¶
type Sequence struct {
Header string //contig id from fasta file
Seq string // contig sequence
NRep []float64 // numerical representation of sequence (Integer representation)
LbpCodes []float64 // lbp intermediate slice
Hist []float64 // Un-normalized LBP histogram
Kmers string
}
func NewSequence ¶
func NewSequence() *Sequence
Create a new sequence. All slices are instantiated as nil slices and speciesID is default zero.
func ReadFasta ¶
Read in a fasta file saving each sequence and header to a unique Sequence type. Store sequences in a slice https://www.socketloop.com/tutorials/golang-bufio-newreader-readline-to-read-file-line-by-line
func (*Sequence) FindLBP ¶
Threshold using signbit function and sliding window of size wind. Wind should be odd and > 0.
func (*Sequence) IntRep ¶
func (seq *Sequence) IntRep()
Create integer representation for a sequence
func (*Sequence) NewHistogram ¶
Calculate the LBP histogram
type SequenceCollection ¶
type SequenceCollection struct {
sync.RWMutex
Items []ReducedSequence
}
http://dnaeon.github.io/concurrent-maps-and-slices-in-go/
func (*SequenceCollection) AddSVD ¶
func (sc *SequenceCollection) AddSVD(svd *Dense)
func (*SequenceCollection) Append ¶
func (cs *SequenceCollection) Append(item ReducedSequence)
func (*SequenceCollection) ToCSV ¶
func (sc *SequenceCollection) ToCSV(fname string)
func (*SequenceCollection) ToParquet ¶
func (sc *SequenceCollection) ToParquet(fname string)
Write results to parquet file. This is the recommended output format.
Source Files
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