Package Bio :: Package Saf
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Package Saf

source code

Parser for SAF (Simple Alignment Format).

This is a fairly liberal multiple sequence alignment format, where record names may contain up to 14 characters and no blanks. Lines beginging with a hash (#) are ignored.

SAF has been described as a simplified subset of MSF, dropping the checksum and with more flexibility in terms of line length.

A current URL describing this file format is: http://www.predictprotein.org/Dexa/optin_saf.html

This appears to replace the old URL of: http://www.embl-heidelberg.de/predictprotein/Dexa/optin_safDes.html

Submodules [hide private]

Classes [hide private]
  Iterator
Iterator interface to move over a file of Saf entries one at a time.
  _Scanner
Start up Martel to do the scanning of the file.
  _RecordConsumer
Create a Saf Record object from scanner generated information.
  RecordParser
Parse Saf files into Record objects.