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Open Source Science

https://github.com/brisvag/cs2star

https://github.com/brisvag/cs2star

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: brisvag
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 71.3 KB
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 3
  • Open Issues: 1
  • Releases: 3
Created over 5 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

cs2star

License PyPI Python Version CI codecov

A simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory. On top of what csparc2star.py already does, this script will traverse the Cryosparc job tree to find the relevant .cs files, automatically symlinks (or copies) the .mrc files (renaming them as appropriate to mrcs and updating the rlnMicrographName column to reflect the change). cs2star also separates micrograph information in a micrographs.star file, which is required in several relion jobs.

Installation

This package requires pyem, which is not available on pip under that name (there is a pyem on pip; that's a different package!). To install it manually [NOTE: some fixes necessary for this are not yet on the main repo, so we're installing from a fork]:

bash pip install git+https://github.com/brisvag/pyem.git

You can then install cs2star with pip:

bash pip install cs2star

Usage

bash cs2star cryosparc_job_dir [dest_dir]

A couple more options are available, check out the help page with -h.

Example

Assuming Cryosparc/J23 is a classification job:

bash cs2star Cryosparc/J23 -p

will create in the working directory: - a relion-ready particles.star - a relion-ready micrographs.star - a patches directory containing the particle images to be used by relion refinement You can now run relion and provide particles.star and micrographs.star as the inputs.

Tips

  • While you can use the --class option to select specific classes from a cryosparc job, the class indexes do not correspond the the class order in Cryosparc (which is simply based on particle number). A much easier way to select specific classes to convert to .star is to use the select 2D classes job in cryosparc, then provide this job as input to cs2star.
  • --swapxy defaults to True. This is because usually that's what you need; unfortunately, this may differ on a case by case basis, so make sure to check the data after conversion with you favourite viewer to ensure that particles are correctly centered.

Owner

  • Name: Lorenzo Gaifas
  • Login: brisvag
  • Kind: user
  • Company: @gutsche-lab

PhD student at @gutsche-lab, doing computational stuff with cryo-ET data.

GitHub Events

Total
  • Watch event: 2
  • Delete event: 1
  • Push event: 1
  • Pull request event: 2
  • Fork event: 1
  • Create event: 1
Last Year
  • Watch event: 2
  • Delete event: 1
  • Push event: 1
  • Pull request event: 2
  • Fork event: 1
  • Create event: 1

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 48
  • Total Committers: 1
  • Avg Commits per committer: 48.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lorenzo Gaifas b****g@g****m 48

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 4
  • Total pull requests: 4
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 14 days
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 1.75
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • haraQQiri (1)
  • unaginekomoyashi (1)
  • SepidehV (1)
  • alisterburt (1)
Pull Request Authors
  • dependabot[bot] (5)
  • brisvag (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (5) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 215 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 30
  • Total maintainers: 1
pypi.org: cs2star

A simple utility to convert cryosparc particle positions to relion star format.

  • Versions: 30
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 215 Last month
Rankings
Dependent packages count: 10.1%
Downloads: 15.7%
Average: 15.8%
Dependent repos count: 21.6%
Maintainers (1)
brisvag
Last synced: 11 months ago

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v4 composite
  • softprops/action-gh-release v1 composite
pyproject.toml pypi
  • click *
  • numpy *
  • pandas *
  • rich *