Csparc2star error removing path uid

Import and Export
1

Hi All,

I’m trying to convert particles extracted in cryosparc using the updated csparc2star.py and I’m running into an error that looks related to the new strip_path_uid function. The command and error are below. Does anyone have suggestions?

-Ryan

./csparc2star.py --swapxy P23_J45_particles_exported.cs from_cs.star

  File "./csparc2star.py", line 128, in <module>
    sys.exit(main(parser.parse_args()))
  File "./csparc2star.py", line 61, in main
    df = star.strip_path_uids(df, inplace=True, count=args.strip_uid)
  File "/home/XXX/pyem/pyem/pyem/star.py", line 699, in strip_path_uids
    df[Relion.MICROGRAPH_NAME] = df[Relion.MICROGRAPH_NAME].str.replace(pat, "", regex=True, count=count)
  File "/home/XXX/pyem/lib/python3.8/site-packages/pandas/core/strings/accessor.py", line 116, in wrapper
    return func(self, *args, **kwargs)
TypeError: replace() got an unexpected keyword argument 'count'
1 Like
2

Hi Ryan,

I have been getting the exact same error since yesterday. I am trying to convert particles that I refined using the newest version of Cryosparc (3.3.1). I can still, however, convert particles processed using previous versions (e.g 3.2.x). Nothing I’ve tried has worked so an update (pyem) may be required to fix?

-Alex

3

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.

Best,

Ryan

4

I’m also getting this error for particles extracted and refined in the newest version of cryosparc (before patch) with updated pyem.

5

I’ve been breaking things again. Sorry. Hopefully all the current difficulties (UIDs, etc) will be resolved in the next few days.

4 Likes
6

Hi Daniel,
Any news on the Csparc2star error?
Thanks,
Gio

7

@gptomaleri Yes, it’s fixed. And the UIDs are being stripped as well. In the future I will add the ability to specify a certain depth of UIDs to keep (since more UIDs are added with each export/import round), for now they will all be removed if --strip-uid is passed.

For --copy-micrograph-coordinates the stripped UIDs are always tried if it fails on the attempt with the raw path names.

3 Likes