# **************************************************************************
# *
# * Authors: Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * MRC Laboratory of Molecular Biology, MRC-LMB
# *
# * 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.protocol.params as params
import pyworkflow.utils as pwutils
from pyworkflow.constants import PROD
import relion.convert as convert
from .protocol_base import ProtRelionBase
[docs]class ProtRelionExportCoordinates(ProtRelionBase):
""" Export coordinates from Relion to be used outside Scipion. """
_label = 'export coordinates'
_devStatus = PROD
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('inputCoordinates', params.PointerParam,
pointerClass='SetOfCoordinates',
important=True,
label="Input coordinates",
help='Select the SetOfCoordinates ')
# --------------------------- INSERT steps functions ----------------------
def _insertAllSteps(self):
objId = self.inputCoordinates.get().getObjId()
self._insertFunctionStep("exportCoordsStep", objId)
# --------------------------- STEPS functions -----------------------------
[docs] def exportCoordsStep(self, coordsId):
""" Create the input file in STAR format as expected by Relion.
If the input particles comes from Relion, just link the file.
"""
pwutils.cleanPath(self._getExportPath())
pwutils.makePath(self._getExportPath())
convert.writeSetOfCoordinates(self._getExportPath(),
self.getCoords(),
self._getMicPos)
# --------------------------- INFO functions ------------------------------
def _validate(self):
validateMsgs = []
return validateMsgs
def _summary(self):
summary = []
summary.append("Output is written to: \n%s\n" %
os.path.abspath(self._getExportPath()))
return summary
# --------------------------- UTILS functions -----------------------------
def _getMicPos(self, mic):
fileName = pwutils.removeBaseExt(mic.getFileName()) + "_coords.star"
return fileName
[docs] def getCoords(self):
return self.inputCoordinates.get()
def _getExportPath(self, *paths):
return os.path.join(self._getPath('Export'), *paths)