# **************************************************************************
# *
# * 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())
seqBio = seqHandler._sequence # Bio.Seq.Seq object
# Step 2: retrieving of the other args needed in the saveFile method
seqID = obj.getId() if obj.getId() is not None else 'seqID'
seqName = obj.getSeqName() if obj.getSeqName() is not None else 'sequence'
seqDescription = obj.getDescription() if obj.getDescription() is not None else ''
# check if protocol has created directory extructura, if not use /tmp
extraDir = self.protocol._getExtraPath()
if os.path.isdir(extraDir):
seqFileName = os.path.abspath(
self.protocol._getExtraPath(seqName + ".fasta"))
else:
seqFileName = os.path.abspath(os.path.join("/tmp", 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)