labblouin.mdsa module

A library to manage interfacing with the MDSA database raw files (http://dna.cs.byu.edu/mdsas/index.shtml).

mdsa Python Library / Oct 8, 2014 / Alex Safatli

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

E-mail: safatli@cs.dal.ca Dependencies: IO, FASTAnet (LabBlouinTools)

class labblouin.mdsa.mdsaAlignment(finame)

Model a single MDSA alignment.

getAlignmentLength()

getFASTAfor(names)

getNames()

getNumSequences()

getObject()

getPath()

getSequenceLength()

getSequences()

writeFASTA(fi, names=None)

class labblouin.mdsa.mdsaDatabase(dbpath, traverse=True)

getFiles()

getPath()

traverse()