Source code for relion.protocols.protocol_gentle_clean

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# * Authors: Grigory Sharov (
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# * MRC Laboratory of Molecular Biology, MRC-LMB
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import os
import re
from glob import glob

from pyworkflow.protocol import Protocol
from pyworkflow.constants import BETA
from pyworkflow.protocol.params import LabelParam

[docs]class ProtRelionCleanJobs(Protocol): """ Run Relion gentle clean procedure for the whole project. """ _label = 'clean project' _devStatus = BETA def __init__(self, **kwargs): Protocol.__init__(self, **kwargs) self.moveDict = dict() # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='Input') form.addParam('desc', LabelParam, label="Gentle clean procedure will move all " "intermediate files from finished Relion " "protocols to Trash folder. For iteration-based " "jobs, only the last iteration files are kept.") # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): self._insertFunctionStep("findRelionProtsStep") self._insertFunctionStep("runCleanStep") self._insertFunctionStep('createOutputStep') # --------------------------- STEPS functions -----------------------------
[docs] def findRelionProtsStep(self): project = self.getProject() runs = project.getRuns() prjPath = os.path.abspath(project.getPath()) if os.path.isdir(os.path.join(prjPath, "Trash")): raise FileExistsError("Folder %s already exists!!!" % os.path.join(prjPath, "Trash")) else: os.makedirs(os.path.join(prjPath, "Trash")) # make a dict with finished Relion protocols protDict = dict() for prot in runs: protCls = prot.getClassName() if prot.getStatus() == "finished" and protCls.startswith("ProtRelion"): extraDir = prot._getExtraPath() if protCls not in protDict: protDict[protCls] = [extraDir] else: protDict[protCls].append(extraDir) if protDict:"Found the following folders:\n") for k, v in protDict.items():"%s: %s" % (k, v)) else: return fnsTemplate = { 'ProtRelionExtractParticles': ['../micrographs_*.star'], 'ProtRelionPostProcess': ['*masked.mrc'], 'ProtRelionMotionCor': ['*', '*.log', '*.TXT'], 'ProtRelionBayesianPolishing': ['*_FCC_cc.mrc', '*_FCC_w0.mrc', '*_FCC_w1.mrc'], 'ProtRelionCtfRefinement': ['*_wAcc_optics-group*.mrc', '*_xyAcc_optics-group*.mrc', '*_aberr-Axx_optics-group_*.mrc', '*_aberr-Axx_optics-group_*.mrc', '*_aberr-Axy_optics-group_*.mrc', '*_aberr-Ayy_optics-group_*.mrc', '*_aberr-bx_optics-group_*.mrc', '*_aberr-by_optics-group_*.mrc', '*_mag_optics-group_*.mrc', '*', '*_fit.eps'], } baseProts = ['ProtRelionClassify2D', 'ProtRelionClassify3D', 'ProtRelionRefine3D', 'ProtRelionInitialModel', 'ProtRelionMultiBody'] for prot in protDict: if prot in fnsTemplate: for protDir in protDict[prot]: for regex in fnsTemplate[prot]: self.moveDict[os.path.join(prjPath, protDir, regex)] = os.path.join(prjPath, "Trash", protDir) elif prot in baseProts: for protDir in protDict[prot]: files = sorted(glob(os.path.join(prjPath, protDir, "relion_?t???_*"))) # Move all files except for the last iteration self.debug(files) result = None if files: s ="_?t(\d{3})_", files[-1]) if s: # group 1 is 3 digits iteration number result = "relion_[ic]t%03d_" % int("I'll keep files: %s from %s" % (result, protDir)) if result: for f in files: match =, f) if not match: self.moveDict[os.path.join(prjPath, protDir, f)] = os.path.join(prjPath, "Trash", protDir)
[docs] def runCleanStep(self): if not self.moveDict:"Did not find any files to remove.") return"Running gentle clean for finished Relion protocols..") for k, v in self.moveDict.items(): try: os.makedirs(v, exist_ok=True) os.system("mv %s %s 2> /dev/null" % (k, v)) except: pass"DONE!")
[docs] def createOutputStep(self): pass
# --------------------------- INFO functions ------------------------------ def _summary(self): if self.isFinished(): prjPath = os.path.abspath(self.getProject().getPath()) return ["Files moved to: *%s*" % os.path.join(prjPath, "Trash")] else: return []