| name | md5fa |
| description | Use when hashing FASTA records and comparing ordered versus order-insensitive sequence digests instead of taking a single whole-file MD5. |
| disable-model-invocation | true |
| user-invocable | true |
md5fa
md5fa is an HTSlib-based FASTA digester. It emits one MD5 per FASTA record plus two aggregate summaries, >ordered and >unordered, so it is materially different from md5sum on the raw file bytes.
Quick Start
- Command:
md5fa <fasta>
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/md5fa
- Live output shape:
md5 fasta_path record_label
When To Use This Tool
- Hash FASTA content at the record level instead of hashing the literal file bytes.
- Compare two FASTA files while distinguishing "same records, different order" from "different sequence content".
- Generate stable per-sequence digests for reference or manifest workflows.
Common Patterns
md5fa sample.fa
md5fa a.fa
md5fa b.fa
md5fa sample.fa > sample.fa.md5fa.txt
Recommended Workflow
- Run
md5fa on a valid FASTA file rather than on arbitrary text.
- Compare the per-record lines first if you need to identify which sequence changed.
- Compare
>ordered when record order is meaningful and >unordered when you only care about the multiset of records.
- Store the full output table, not just one line, because the aggregate summaries capture different invariants.
Guardrails
md5fa -h is not help; it is treated as a filename and errors with md5fa: -h: No such file or directory.- This is not a whole-file checksum tool. A multi-record FASTA produces one digest per record plus
>ordered and >unordered.
- In live testing, swapping the order of two FASTA records changed the
>ordered digest but left >unordered unchanged.
- An empty FASTA emitted the normal empty MD5 for
>ordered (d41d8cd98f00b204e9800998ecf8427e) and an all-zero digest for >unordered.
- Output includes three fields: digest, source FASTA path, and record label. Downstream parsers should not assume a plain two-column
md5sum layout.
