Pathoplexus Tools

Configuration File: pathoplexus_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the pathoplexus_tools.json configuration file.

Available Tools

Pathoplexus_count_sequences (Type: PathoplexusCountTool)

Count and aggregate open pathogen genome sequences in Pathoplexus (LAPIS) for genomic-epidemiolog…

Pathoplexus_count_sequences tool specification

Tool Information:

  • Name: Pathoplexus_count_sequences

  • Type: PathoplexusCountTool

  • Description: Count and aggregate open pathogen genome sequences in Pathoplexus (LAPIS) for genomic-epidemiology surveillance of emerging pathogens. Returns sequence counts for an organism, optionally filtered by country and lineage and grouped by a metadata field (e.g. geoLocCountry, lineage, sampleCollectionDate) to see geographic/temporal distribution. Known organisms: ‘west-nile’, ‘ebola-zaire’, ‘ebola-sudan’, ‘cchf’ (Crimean-Congo hemorrhagic fever), ‘mpox’. No API key required.

Parameters:

  • organism (string) (required) Pathoplexus organism slug: ‘west-nile’, ‘ebola-zaire’, ‘ebola-sudan’, ‘cchf’, ‘mpox’.

  • country ([‘string’, ‘null’]) (optional) Filter by country (geoLocCountry), e.g. ‘USA’.

  • lineage ([‘string’, ‘null’]) (optional) Filter by lineage.

  • group_by ([‘string’, ‘null’]) (optional) Metadata field to group counts by, e.g. ‘geoLocCountry’, ‘lineage’, ‘sampleCollectionDate’.

Example Usage:

query = {
    "name": "Pathoplexus_count_sequences",
    "arguments": {
        "organism": "example_value"
    }
}
result = tu.run(query)

Pathoplexus_get_mutations (Type: PathoplexusMutationsTool)

Get characteristic amino-acid (default) or nucleotide mutations for a Pathoplexus organism above …

Pathoplexus_get_mutations tool specification

Tool Information:

  • Name: Pathoplexus_get_mutations

  • Type: PathoplexusMutationsTool

  • Description: Get characteristic amino-acid (default) or nucleotide mutations for a Pathoplexus organism above a proportion threshold, optionally filtered by country/lineage — for surveillance of mutation prevalence in emerging pathogens. Returns each mutation with gene, position, from/to residue, proportion (fraction of sequences carrying it), count, and coverage. Known organisms: ‘west-nile’, ‘ebola-zaire’, ‘ebola-sudan’, ‘cchf’, ‘mpox’. No API key required.

Parameters:

  • organism (string) (required) Pathoplexus organism slug, e.g. ‘west-nile’, ‘mpox’.

  • country ([‘string’, ‘null’]) (optional) Filter by country (geoLocCountry).

  • lineage ([‘string’, ‘null’]) (optional) Filter by lineage.

  • min_proportion ([‘number’, ‘null’]) (optional) Minimum proportion of sequences carrying the mutation (default 0.8).

  • mutation_type ([‘string’, ‘null’]) (optional) ‘aminoAcid’ (default) or ‘nucleotide’.

  • limit ([‘integer’, ‘null’]) (optional) Max mutations (default 50, max 500).

Example Usage:

query = {
    "name": "Pathoplexus_get_mutations",
    "arguments": {
        "organism": "example_value"
    }
}
result = tu.run(query)

Pathoplexus_get_sequence_details (Type: PathoplexusCountTool)

List the individual sequence records (not aggregated counts) behind a Pathoplexus organism, from …

Pathoplexus_get_sequence_details tool specification

Tool Information:

  • Name: Pathoplexus_get_sequence_details

  • Type: PathoplexusCountTool

  • Description: List the individual sequence records (not aggregated counts) behind a Pathoplexus organism, from the LAPIS /details endpoint. Returns a per-sequence metadata table — accession, country (geoLocCountry), collection date (sampleCollectionDate), host, lineage, clade and any other requested fields — so you can enumerate the actual surveilled genomes rather than only their totals. Optionally filter by country and lineage and select which fields to return. Known organisms: ‘west-nile’, ‘ebola-zaire’, ‘ebola-sudan’, ‘cchf’, ‘mpox’. No API key required.

Parameters:

  • organism (string) (required) Pathoplexus organism slug: ‘west-nile’, ‘ebola-zaire’, ‘ebola-sudan’, ‘cchf’, ‘mpox’.

  • country ([‘string’, ‘null’]) (optional) Filter by country (geoLocCountry), e.g. ‘USA’.

  • lineage ([‘string’, ‘null’]) (optional) Filter by lineage.

  • fields ([‘string’, ‘null’]) (optional) Comma-separated metadata fields to return, e.g. ‘accession,geoLocCountry,sampleCollectionDate,lineage’. Omit to return all available fields.

  • limit ([‘integer’, ‘null’]) (optional) Max sequence rows (default 50, max 1000).

  • offset ([‘integer’, ‘null’]) (optional) Row offset for pagination (default 0).

Example Usage:

query = {
    "name": "Pathoplexus_get_sequence_details",
    "arguments": {
        "organism": "example_value"
    }
}
result = tu.run(query)

Pathoplexus_get_sequences_fasta (Type: PathoplexusCountTool)

Download the actual genome sequences (FASTA) from Pathoplexus/LAPIS for a surveilled pathogen. Re…

Pathoplexus_get_sequences_fasta tool specification

Tool Information:

  • Name: Pathoplexus_get_sequences_fasta

  • Type: PathoplexusCountTool

  • Description: Download the actual genome sequences (FASTA) from Pathoplexus/LAPIS for a surveilled pathogen. Returns unaligned (default) or aligned nucleotide or amino-acid sequences as FASTA text, optionally filtered by country and lineage. This is the only way in ToolUniverse to retrieve the nucleotide/protein sequence of Pathoplexus genomes — the other tools expose only counts and mutations. Known organisms: ‘west-nile’, ‘ebola-zaire’, ‘ebola-sudan’, ‘cchf’, ‘mpox’. No API key required.

Parameters:

  • organism (string) (required) Pathoplexus organism slug: ‘west-nile’, ‘ebola-zaire’, ‘ebola-sudan’, ‘cchf’, ‘mpox’.

  • country ([‘string’, ‘null’]) (optional) Filter by country (geoLocCountry), e.g. ‘USA’.

  • lineage ([‘string’, ‘null’]) (optional) Filter by lineage.

  • sequence_type ([‘string’, ‘null’]) (optional) ‘nucleotide’ (default) or ‘aminoAcid’.

  • aligned ([‘boolean’, ‘null’]) (optional) Return aligned sequences instead of unaligned (default false).

  • limit ([‘integer’, ‘null’]) (optional) Number of sequences to download (default 1, max 100).

Example Usage:

query = {
    "name": "Pathoplexus_get_sequences_fasta",
    "arguments": {
        "organism": "example_value"
    }
}
result = tu.run(query)