v1.1.0

v1.1.0: Mutations

This new version includes the Scop3P's endpoint "mutations" to fetch the list of related mutations to a queried entry.

usage: scop3p [-h] --accession ACCESSION [--version] [-v API_VERSION] [--log-file LOG_FILE] [--raw]
              [--no-cache] [--cache-ttl CACHE_TTL] [--indent INDENT] [--separator SEPARATOR]
              [--no-header] [--null-value NULL_VALUE] [--save TARGET:FORMAT:PATH]
              [--include-structures] [--include-peptides] [--include-mutations]

The official Scop3P REST API Python client (v1.1.0)

options:
  -h, --help            show this help message and exit
  --accession ACCESSION
                        UniProtKB accession number (e.g., O00571)
  --version             Show package version and exit
  -v, --api-version API_VERSION
                        API version to pass as query parameter (e.g. O00571)
  --log-file LOG_FILE   File to save FAIR provenance log (default: output.log)
  --raw                 Print raw JSON without pretty formatting (only for json format)
  --no-cache            Bypass cache and force a network request (still may write cache)
  --cache-ttl CACHE_TTL
                        Cache TTL in seconds (default: 300)
  --indent INDENT       JSON indentation size (default: 2, only for json format)
  --separator SEPARATOR
                        Column separator for tabular formats (default: tab)
  --no-header           Omit header row in tabular output
  --null-value NULL_VALUE
                        String representation for None/missing values in tabular formats (default:
                        'None')
  --save TARGET:FORMAT:PATH
                        Save additional outputs in a single run. TARGET:
                        modifications|structures|peptides|mutations, FORMAT: json|tsv
  --include-structures  Include structures in stdout JSON output (also implied by --save
                        structures:...)
  --include-peptides    Include peptides in stdout JSON output (also implied by --save peptides:...)
  --include-mutations   Include mutations in stdout JSON output (also implied by --save mutations:...)

Example

Command: scop3p --accession 'Q5T0W9' --include-mutations

"mutations": [
      {
        "position": 410,
        "pdbIds": {},
        "referenceAA": "N",
        "altAA": "S",
        "type": "Polymorphism",
        "disease": ""
      },
      {
        "position": 435,
        "pdbIds": {},
        "referenceAA": "S",
        "altAA": "R",
        "type": "Polymorphism",
        "disease": ""
      },
      {
        "position": 640,
        "pdbIds": {},
        "referenceAA": "K",
        "altAA": "T",
        "type": "Polymorphism",
        "disease": ""
      },
      {
        "position": 907,
        "pdbIds": {},
        "referenceAA": "T",
        "altAA": "N",
        "type": "Polymorphism",
        "disease": ""
      }
    ]

What's Changed

• Add new gh action by @agdiaz in #3
• Add mutations endpoint by @agdiaz in #2

Full Changelog: v1.0.1...v1.1.0

v1.0.1

What's new ?

Fixes related to metadata files (Readme) and Project metadata (wrong links).

Full Changelog: v1.0.0...v1.0.1

Initial version: v1.0.0

The official Scop3P REST API Python client

Initial version: v1.0.0

Added

The official Scop3P REST API Python client, developed and maintained by CompOmics and Bio2Byte, provides CLI and Python interfaces to retrieve phospho-site modifications, structures, and peptides with cache-aware requests, JSON/TSV exports, and FAIR provenance logging for reproducible analysis.