smtext

Documentation

Overview

Package smtext handles text representations of substitution matrices.

NCBI Format

This is the format used in ftp://ftp.ncbi.nih.gov/blast/matrices/. Example:

# Optional comment line.
# Another optional comment line.
   A  C  G  T
A  1 -2 -1 -2
C -2  1 -2 -1
G -1 -2  1 -2
T -2 -1 -2  1

Specifically:

Empty lines and lines beginning with '#' are ignored. Each line should have its values separated by whitespaces (any kind and any amount). The first line should have n letters. The others need to have n+1 values, where the first is a letter and the rest are float-parseable numbers.

Index

• func ReadNCBI(r io.Reader) (align.SubstitutionMatrix, error)

Functions

func ReadNCBI

func ReadNCBI(r io.Reader) (align.SubstitutionMatrix, error)

ReadNCBI decodes an NCBI-format substitution matrix from the given reader.