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.
Variables [hide private]
  __warningregistry__ = {('Bio.Saf has been deprecated, due to p...
Variables Details [hide private]

__warningregistry__

Value:
{('Bio.Saf has been deprecated, due to problems with Martel and recent\
 versions of mxTextTools. If you want to continue to use this module (\
or read this file format), please get touch to avoid permanent removal\
 of this module from Biopython.',
  <type 'exceptions.DeprecationWarning'>,
  26): 1}