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Feature #8747

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Upload particle coordinates from single Relion star file

Added by William Rice over 4 years ago. Updated over 4 years ago.

Status:
Assigned
Priority:
Normal
Assignee:
Category:
-
Start date:
03/09/2020
Due date:
% Done:

0%

Estimated time:

Description

Current upload coordinates command only lets you upload a list of starfiles, with the assumption that the micrograph name is encoded in the star filename (e.g. foo_gr_867_sq_5_hl_309_enn-a-DW.star). Particles picked by some programs, such as Warp, output a single star file with filename listed on each line in the appropriate relion column.

This change now treats a single uploaded file as such a starfile, so it processes inputs of a single file as a star file with a rln_MicrographName column properly.

Note: Uploading a single EMAN boxfile or a single relion starfile without a rln_MicrographName column will now fail, but this is likely a very rare problem

Actions #1

Updated by William Rice over 4 years ago

  • Tracker changed from Bug to Feature
  • Affected Version deleted (Appion/Leginon 3.5)
  • Show in known bugs deleted (No)
Actions #2

Updated by William Rice over 4 years ago

  • Description updated (diff)
Actions #3

Updated by William Rice over 4 years ago

  • Description updated (diff)
Actions #4

Updated by Anchi Cheng over 4 years ago

  • Status changed from New to Assigned
  • Assignee set to William Rice
  • Target version set to Appion/Leginon 3.5

Bill,
I changed the first line of text to use python specified by /usr/bin/env like all other python code in Appion.

Hope that does not cause problems for you.

Actions #5

Updated by William Rice over 4 years ago

No problem, sorry about that. I have tested it several times now and it has not run into any issues uploading star files from Warp.

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