PySAT: Python Seqeuence Analysis Tools (Version 1.0)

Python is an Object oriented scripting language. Simple, ease of use and clear syntax makes it desirable. PySAT is a collection of bioinformatics tools written entirely in python. You need python version 1.5.2 and above. I tested the modules with python 2.0 and they are okey !

Currently PySAT has

• 'database' is an abstract module to handle flat file databases of different format (EMBL, GENBANK, SWISSPROT, FASTA, ...). This module needs regular expression based parser (check out embl_parser.py, genbank_parser.py, etc.,) and a definition file (eg., embl.d, genbank.d). The next version of PySAT will repalace these .d files to .py files to make it more simple to handle definition files (anyway they are not more than few lines).

  If you have a new flat file database to be used with PySAT, you have to

  • write the parser for it
  • and write the definition file

• classseq module to make and print sequence objects in different formats (embl, swissprot, genbank, staden, gcg, fasta, ...)

• and few other modules for creating and iterating over "feature table" objects.

Send me your suggestions!

Object-oriented parsing of biological databases with Python
Chenna Ramu, et. al.
Bioinformatics, Volume 16, Issue 7, Pages 628-638 : July 2000