Source code for pwem.viewers.viewer_sequence

# **************************************************************************
# *
# * Authors:     Roberto Marabini (roberto@cnb.csic.es)
# *              Marta Martinez (mmmtnez@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************

import os

import pyworkflow.viewer as pwviewer
from pyworkflow.gui.text import openTextFileEditor

import pwem.objects as emobj
import pwem.convert as emconv


[docs]class SequenceViewer(pwviewer.Viewer): """ Wrapper to visualize Sequences with an editor. """ _environments = [pwviewer.DESKTOP_TKINTER] _targets = [emobj.Sequence] def __init__(self, **kwargs): pwviewer.Viewer.__init__(self, **kwargs) # def visualize(self, obj, **kwargs): # fn = obj.getFileName() # openTextFileEditor(fn)
[docs] def visualize(self, obj, **kwargs): # The sequence object is visualized in a tmp file; # To build this tmp file we use a method (saveFile) from the class # SequenceHandler that requires a Biopython sequence (Bio.Seq.Seq # object); # Step 1: transformation of the sequence of our Scipion Sequence # object (obj.getSequence()) in a Biopython Sequence: # Let keep the SequenceHandler import here to avoid a default BioPython # import seqHandler = emconv.SequenceHandler(obj.getSequence(), isAminoacid=obj.getIsAminoacids()) seqBio = seqHandler._sequence # Bio.Seq.Seq object # Step 2: retrieving of the other args needed in the saveFile method seqID = obj.getId() seqName = obj.getSeqName() seqDescription = obj.getDescription() seqFileName = os.path.abspath( self.protocol._getExtraPath(seqName + ".fasta")) # Step 3: Sequence saved in the extra file seqHandler.saveFile(seqFileName, seqID, sequence=seqBio, name=seqName, seqDescription=seqDescription, type="fasta") # Step 4: Visualization of extra file openTextFileEditor(seqFileName)