hmm

Documentation

Overview

Package hhm parses hhm files generated by the HHsuite programs. (i.e., hhmake, hhsearch, hhblits, etc.)

Each HHM file can be thought of as contain four logical sections: 1) The header with meta information about the HMM. 2) Optional secondary structure information from DSSP and/or PSIPED. 3) A multiple sequence alignment in A3M format. 4) The HMM formatted similarly to HMMER's hmm files, but without pseudo counts.

Index

• func WriteHHM(w io.Writer, hhm *HHM) error
• func WriteHMM(w io.Writer, hmm *HMM) error
• type HHM
  • func ReadHHM(r io.Reader) (*HHM, error)
  • func (hhm *HHM) Slice(start, end int) *HHM
• type HHMSecondary
  • func (ss HHMSecondary) Slice(start, end int) HHMSecondary
• type HMM
  • func ReadHMM(r io.Reader) (*HMM, error)
• type Meta

Functions

func WriteHHM

func WriteHHM(w io.Writer, hhm *HHM) error

WriteHHM writes an hmm file that can be read by HHsuite programs (i.e., hhblits, hhsearch, etc).

func WriteHMM

func WriteHMM(w io.Writer, hmm *HMM) error

WriteHMM writes an hmm file that can be read by HMMER.

Currently, this function is broken. Do not use.

Types

type HHM

type HHM struct {
	Meta      Meta
	Secondary HHMSecondary
	MSA       seq.MSA
	HMM       *seq.HMM
}

HHM corresponds to an hhm file produce by HHsuite (i.e., hhblits or hhmake).

func ReadHHM

func ReadHHM(r io.Reader) (*HHM, error)

func (*HHM) Slice

func (hhm *HHM) Slice(start, end int) *HHM

Slice dices up an entire HHM file. The slice indices should be in terms of the number of match/delete states in the underlying HMM. All secondary structure annotations are also sliced. The multiple sequence alignment is also sliced. The NEFF for the HHM is also re-computed as the average of all NeffM scores in each HMM column.

type HHMSecondary

type HHMSecondary struct {
	SSdssp    *seq.Sequence
	SAdssp    *seq.Sequence
	SSpred    *seq.Sequence
	SSconf    *seq.Sequence
	Consensus *seq.Sequence
}

An HHMSecondary represents secondary structure information that *may* be in an HHM file. Any or all members of an HHMSecondary may be nil.

func (HHMSecondary) Slice

func (ss HHMSecondary) Slice(start, end int) HHMSecondary

Slice will create a new collection of secondary structure sequences where each sequence has been sliced with the given start/end parameters.

type HMM

type HMM struct {
	Meta Meta
	HMM  *seq.HMM
}

HMM corresponds to an hmm file produced by HMMER.

func ReadHMM

func ReadHMM(r io.Reader) (*HMM, error)

ReadHMM reads an hmm file produced by HMMER.

Currently, this function is broken. Do not use.

type Meta

type Meta struct {
	// Corresponds to the HHsearch version for which this format was
	// first introduced.
	FormatVersion string

	// The name of the HMM and an optional description.
	Name string

	// Family if the sequence is from SCOP or PFAM.
	Fam string

	// Command that was used to generate the file.
	Com string

	// Diversity of the alignment, calculated as the exp of the negative
	// entropy averaged over all columns of the alignment.
	Neff seq.Prob

	// ???
	File string

	// Number of match states and number of columns. Doesn't appear to be
	// in machine readable format.
	Leng string

	// Pre-filter details? Not machine readable.
	Filt string

	// EVD parameters. (Not used in HHsuite 2+, I think.)
	EvdLambda, EvdMu float64

	// Whether the HMM has pseudo count correction.
	Pct bool

	// Date file was generated.
	// e.g., 'Sat Nov 10 21:31:12 2012'
	Date string

	// ???
	Desc string
}