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Document gene and fragment FASTA inputs - #26
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The documentation accurately reflects the V2 and legacy input behavior with no unresolved issues.
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What changed in this PR
Documents nucleotide FASTA inputs for V2 motif inference and distinguishes them from protein FASTAs and legacy CLI inputs.
Changes:
- Adds FASTA syntax, fragment handling, and DNA-symbol guidance.
- Provides a Biopython V2 loading example.
- Links the guide from the README and documentation index.
| File | Description |
|---|---|
README.md |
Links to the new FASTA guide. |
docs/user_guide.rst |
Adds comprehensive gene/TF FASTA documentation. |
docs/index.rst |
Includes the guide in the documentation tree. |
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Issue #19 asks for basic instructions on input FASTA files: one file per gene or transcription factor, optionally multi-FASTA when the gene is in fragments, in which case every fragment is run through the pipeline. Add a short Input FASTA files subsection under How to Use in the README, next to the -f argument, linking to the fuller Sphinx guide. Trim the guide: plain example headers, a shorter whitespace note, a line on when one-file-per-gene is required versus a convention, and drop the closing sentences that referred to a CLI and to an unrelated benchmark.
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Summary
Document one FASTA file per gene/transcription factor, including multi-record files containing fragments of the same gene.
Explain FASTA syntax, supported DNA symbols, loading records for the V2 API, and how fragments are searched independently without assembly or splicing. Distinguish gene DNA inputs from protein FASTAs and legacy CLI usage.