Csparc2star error removing path uid

RyanFeathers · December 22, 2021, 1:26am

Hi Alex,

This error was from the updated version of pyem that should be able to handle the numbers in the paths. It’s not really a solution but I was able to work around this by using the older version of pyem to get a converted file containing UIDs and then use a search and replace script to remove those.

Update: here’s my script incase it’s helpful.

github.com

ryanfeathers/CryoEM_Scripts/blob/main/repairpaths.py

#!/usr/bin/env python
"""
Replace rlnImageName and rlnMicrographName paths 
Author: Ryan Feathers jrf296
Date: 12/21/2021
"""
import argparse
import starfile
import os.path
import re
import pandas as pd


parser = argparse.ArgumentParser()
parser.add_argument('--i', type=str, required=True, help='input particle star file')
parser.add_argument('--p', type=str, required=False, help='input star file with new paths')
parser.add_argument('--o', type=str, required=True, help='output file name')   
parser.add_argument('--nouid', nargs='?', const=1, type=int, help = 'removeuid')              
args = parser.parse_args()

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Best,

Ryan