lightmotif_io

Module transfac

Source
Expand description

Parser implementation for the TRANSFAC format.

The TRANSFAC matrix format is similar to the EMBL sequence format, using a 2-letter header before each row that is used for metadata. The matrix usually contains counts, but they may be in floating-point format if they were rescaled.

AC  M00005
XX
DT  19.10.1992 (created); ewi.
CO  Copyright (C), Biobase GmbH.
XX
P0      A      C      G      T
01      3      0      0      2      W
02      1      1      3      0      G
03      3      1      1      0      A
04      2      1      2      0      R
05      1      2      0      2      Y
06      0      5      0      0      C
07      5      0      0      0      A
XX

The parser implemented in this module is not complete, and only supports the following metadata:

  • ID: identifier
  • AC: accession
  • NA: name
  • DE: description
  • DT: date (creation or update)
  • RE: references (similar to EMBL in format)
  • BS: binding sites
  • P0: matrix.

Structs§

Date
Reader
A reader for TRANSFAC-formatted files.
Record
A TRANSFAC record.
Reference
ReferenceNumber

Enums§

DateKind

Functions§

read