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rewire-bio

genomics-mcp

Official
by rewire-bio

get_sequence

Read-only

Retrieve the reference sequence for a specified genomic interval from an indexed FASTA file using a file descriptor and interval coordinates.

Instructions

Reference sequence for an interval from an indexed FASTA. Not implemented in this build: returns error code 'unsupported' (E3).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
fileYes
intervalYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
dataNo
errorNoSet when status is error.
errorsNoPer-source failures in partial results.
limitsNo
statusYes
warningsNo
operationYes
provenanceNo
truncationNo
source_statusNo
schema_versionNo1

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

A4.2/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The description adds the critical behavioral detail that the tool is not implemented and returns an error. This goes beyond the annotations (readOnlyHint, openWorldHint), which do not capture the unsupported status. The description discloses exactly what happens on invocation, which is essential for an agent deciding whether to call it.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is only two sentences, front-loaded with the purpose, and immediately reveals the critical 'not implemented' caveat. There is no wasted text; every word contributes to the agent's understanding.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given that the tool is not implemented, the description is complete: it states the intended behavior and the actual (error) outcome. The output schema exists, so return format is available elsewhere. The description leaves no ambiguity about whether to call this tool, which is the most important context here.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate for missing parameter explanations. It only mentions 'indexed FASTA' and 'interval,' which gives minimal context but does not explain the required properties (file, interval) or their nested types. The schema's $defs do provide descriptions, but per the 0% direct coverage signal, the description should have added more parameter detail. It is insufficient.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb and resource: 'Reference sequence for an interval from an indexed FASTA.' This clearly distinguishes it from sibling tools like get_reads or get_coverage, which target different data types. The additional note about being 'not implemented' further clarifies its current state without confusing its intended purpose.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly says 'Not implemented in this build: returns error code unsupported (E3),' which tells the agent not to use it. While it does not name a specific alternative tool, the exclusion is clear and unambiguous, guiding the agent to avoid this tool and try others.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.