Load A3M¶
Loads an A3M multiple sequence alignment (MSA) provided as a raw text string and labels it with a user-defined ID. Outputs a dictionary-style A3M object keyed by the provided ID, suitable for downstream biotech/protein modeling nodes.
Usage¶
Use this node when you already have an A3M MSA (e.g., from external alignment tools) and need to inject it into a workflow. Provide the full A3M text and assign a unique ID so downstream nodes can reference the correct alignment.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| a3m_string | True | STRING | The full A3M MSA content as plain text. Include all alignment lines exactly as produced by your MSA tool. | >query AAAAAAAAAA >homolog1 AA-A-AAA-A |
| a3m_id | True | STRING | Identifier assigned to this A3M MSA. Should be unique within the workflow. If pairing with a specific protein sequence, use a matching sequence ID for clarity. | msa |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| msa.a3m | A3M | A dictionary-like A3M object mapping the provided ID to the A3M text, ready for downstream nodes. | {"msa": ">query\nAAAAAAAAAA\n>homolog1\nAA-A-AAA-A"} |
Important Notes¶
- Unique IDs: Ensure a3m_id values are unique across the workflow to avoid collisions when combining or batching inputs.
- Format integrity: Provide the A3M in its original text format; do not modify line wrapping, headers, or gap characters.
- Sequence pairing: If this A3M corresponds to a specific sequence input elsewhere, align the IDs for easier tracking and compatibility.
Troubleshooting¶
- Empty or malformed A3M: If downstream nodes fail, verify that a3m_string is non-empty and follows valid A3M formatting (headers and aligned sequences).
- ID conflicts: If later nodes report duplicate keys or unexpected merges, change a3m_id to a unique value.
- Unexpected downstream behavior: Confirm that the A3M corresponds to the intended sequence (e.g., matching query sequence) to prevent misalignment issues.