def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
md = MetaData(args.i)
if md.version != "3.1":
self.error("Input file '%s' is not RELION 3.1 format." % args.i)
new_particles = []
print("Reading in input star file.....")
particles = self.get_particles(md)
optic_groups = self.get_optic_groups(md)
print("Total %s particles in input star file." % str(len(particles)))
print("Total %s optic groups found in input star file." %
str(len(optic_groups)))
new_particles.extend(self.rel30format(particles, optic_groups))
mdOut = MetaData()
particleTableName = "data_"
mdOut.addDataTable(particleTableName)
mdOut.addLabels(particleTableName, md.getLabels("data_particles"))
mdOut.addLabels(particleTableName, [
'rlnVoltage', 'rlnSphericalAberration', 'rlnAmplitudeContrast',
'rlnMagnification', 'rlnDetectorPixelSize', 'rlnOriginX',
'rlnOriginY', 'rlnBeamTiltClass'
])
mdOut.removeLabels(
"data_", ['rlnOpticsGroup', 'rlnOriginXAngst', 'rlnOriginYAngst'])
mdOut.addData(particleTableName, new_particles)
mdOut.write(args.o)
print("New star file %s in RELION 3.0 format created. Have fun!" %
args.o)
def main(self):
self.define_parser()
args = self.parser.parse_args()
self.validate(args)
print("Removing columns fromstar file....")
md = MetaData(args.i)
md.removeLabels("data_particles", "rlnImageName", "rlnMicrographName",
"rlnMagnification", "rlnDetectorPixelSize",
"rlnCtfFigureOfMerit", "rlnVoltage", "rlnDefocusU",
"rlnDefocusV", "rlnDefocusAngle",
"rlnSphericalAberration", "rlnCtfBfactor",
"rlnCtfScalefactor", "rlnPhaseShift",
"rlnAmplitudeContrast")
md.write(args.o)
print("New star file " + args.o + " created. Have fun!")
