GitHub

Shoji

Shoji is a a flexible command-line toolset for the analysis of iCLIP and eCLIP sequencing data. It is designed as a replacement for htseq-clip, providing streamlined workflows for annotation parsing, crosslink site extraction, counting, and matrix generation.

Installation

pip install shoji

Features

  • Annotation Parsing: Extract and flatten features from GFF3 files to BED format.
  • Sliding Window Generation: Create sliding windows over genomic annotations for downstream analysis.
  • Crosslink Extraction: Extract crosslink sites from BAM files with flexible options for site type, mate, and filtering.
  • Counting: Count crosslink sites per window and output results in Apache Parquet format.
  • Matrix Creation: Aggregate counts across samples into R-friendly matrices (CSV or Parquet).
  • Tabix Conversion: Convert BED files to bgzipped, tabix-indexed format for efficient querying.

Major differences to htseq-clip

  • No --splitExons flag, Shoji cannot split exons into components
  • New --split-intron flag. If an intron overlaps exon from another gene, using this tag will split the intron into non overlapping chunks
  • Piping output disabled. Output file names MUST be specified
  • count function output is only available in Apache parquet format
  • createMatrix by default do not write duplicate windows. If adjacent overlapping windows have same crosslink counts across all samples, this function now writes only the most 5' (relative to strand) window to output file.

Developed at Hentze lab, EMBL Heidelberg

Name inspired from: Shoji

Project links

Data verified by PyPI on Aug 4, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for biohentze from gravatar.com biohentze

Credits

Author: Sudeep Sahadevan

GitHub Statistics

Data verified by PyPI on Aug 4, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT)

Requires

Python <4.0, >=3.11

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

shoji-0.47.0.tar.gz (41.7 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

shoji-0.47.0-py3-none-any.whl (49.3 kB view details)

Uploaded Python 3

File details

Details for the file shoji-0.47.0.tar.gz.

File metadata

  • Download URL: shoji-0.47.0.tar.gz
  • Upload date:
  • Size: 41.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for shoji-0.47.0.tar.gz
Algorithm Hash digest
SHA256 49ed3014feeb95eeebc14f043b4162674e6d68f09278b4a22371bb8e2bd31366
MD5 9be0fc121e1df9d8462aff810cb219d6
BLAKE2b-256 0820052b2bfca4fa51561e86a57fe6b45f7b1156d8b2d257280a32cd0494194e

See more details on using hashes here.

Provenance

The following attestation bundles were made for shoji-0.47.0.tar.gz:

Publisher: build_publish.yml on EMBL-Hentze-group/Shoji

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file shoji-0.47.0-py3-none-any.whl.

File metadata

  • Download URL: shoji-0.47.0-py3-none-any.whl
  • Upload date:
  • Size: 49.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for shoji-0.47.0-py3-none-any.whl
Algorithm Hash digest
SHA256 ea3d31088cc97583c4221389344f8aa73530a5aa863dc7f7985ea9f31c2acf9e
MD5 4df426d835b9b0095072b1143bf56d72
BLAKE2b-256 5290bb2bd59232cbb43b3e4fdef67dab4b92efd0bbc983a14eb075b11a509df7

See more details on using hashes here.

Provenance

The following attestation bundles were made for shoji-0.47.0-py3-none-any.whl:

Publisher: build_publish.yml on EMBL-Hentze-group/Shoji

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page