Getting Started

This page is for end users who want to query Scop3P quickly from the command line.

Requirements

  • Python >=3.6,<4
  • Internet access to iomics.ugent.be

Installation

Install from PyPI:

python -m pip install scop3p

Run help:

scop3p --help

Quick CLI Usage

Fetch modifications for one UniProt accession:

scop3p --accession O95755

Use a specific API version for modifications:

scop3p --accession O95755 --api-version 1

Include structures, peptides, and mutations in standard output JSON:

scop3p --accession O95755 --include-structures --include-peptides --include-mutations

Save additional files in one run:

scop3p --accession O95755 \
  --save modifications:tsv:modifications.tsv \
  --save structures:tsv:structures.tsv \
  --save peptides:json:peptides.json \
  --save mutations:tsv:mutations.tsv

Cache Controls

Default cache TTL is 300 seconds.

Bypass cache reads:

scop3p --accession O95755 --no-cache

Set custom TTL:

scop3p --accession O95755 --cache-ttl 600

Output And Log Behavior

  • Default output (no --save) is JSON to stdout.
  • --raw prints compact JSON.
  • --indent controls pretty JSON indentation.
  • --save TARGET:FORMAT:PATH writes extra dataset outputs.
  • A FAIR provenance log is written by default to output.log.
  • Use --log-file to customize log path.

Example:

scop3p --accession O95755 --log-file run-fair.log --raw

What --save Supports

  • Targets: modifications, structures, peptides, mutations
  • Formats: json, tsv
  • Mutations TSV columns: position, pdbIds, referenceAA, altAA, type, disease

Examples:

scop3p --accession O95755 --save modifications:json:results.json
scop3p --accession O95755 --save peptides:tsv:peptides.tsv --no-header