Command Mapping
===============

This page maps CLI commands to their parser, handler, client, server route, and core implementation.

Server
------

- ``modalysis server`` -> ``cli/parsers/server.py`` -> ``cli/handlers/server.py`` -> launches FastAPI app in ``server/main.py``.

GFF
---

- ``modalysis gff format`` -> ``cli/parsers/gff.py`` -> ``cli/handlers/gff.py`` -> ``client/gff.py::gff_format`` -> ``server/gff.py::gff_format`` -> ``core/gff.py::format``
- ``modalysis gff annotate`` -> ``cli/parsers/gff.py`` -> ``cli/handlers/gff.py`` -> ``client/gff.py::gff_annotate`` -> ``server/gff.py::gff_annotate`` -> ``core/gff.py::annotate``

Pileup
------

- ``modalysis pileup format`` -> ``cli/parsers/pileup.py`` -> ``cli/handlers/pileup.py`` -> ``client/pileup.py::pileup_format`` -> ``server/pileup.py::pileup_format`` -> ``core/pileup.py::format``
- ``modalysis pileup merge`` -> ``cli/parsers/pileup.py`` -> ``cli/handlers/pileup.py`` -> ``client/pileup.py::pileup_merge`` -> ``server/pileup.py::pileup_merge`` -> ``core/pileup.py::merge``

DMR
---

- ``modalysis dmr format`` -> ``cli/parsers/dmr.py`` -> ``cli/handlers/dmr.py`` -> ``client/dmr.py::dmr_format`` -> ``server/dmr.py::dmr_format`` -> ``core/dmr.py::format``
- ``modalysis dmr annotate`` -> ``cli/parsers/dmr.py`` -> ``cli/handlers/dmr.py`` -> ``client/dmr.py::dmr_annotate`` -> ``server/dmr.py::dmr_annotate`` -> ``core/dmr.py::annotate``
- ``modalysis dmr gene-counts`` -> ``cli/parsers/dmr.py`` -> ``cli/handlers/dmr.py`` -> ``client/dmr.py::dmr_gene_counts`` -> ``server/dmr.py::dmr_gene_counts`` -> ``core/dmr.py::gene_counts``
- ``modalysis dmr common-genes`` -> ``cli/parsers/dmr.py`` -> ``cli/handlers/dmr.py`` -> ``client/dmr.py::dmr_common_genes`` -> ``server/dmr.py::dmr_common_genes`` -> ``core/dmr.py::common_genes``

Plot
----

- ``modalysis plot mean-methylation`` -> ``cli/parsers/plot.py`` -> ``cli/handlers/plot.py`` -> ``client/plot.py::plot_mean_methylation`` -> ``server/plot.py::plot_mean_methylation`` -> ``core/plots/mean_methylation.py::plot_mean_methylation``
- ``modalysis plot gene-heatmap`` -> ``cli/parsers/plot.py`` -> ``cli/handlers/plot.py`` -> ``client/plot.py::plot_gene_heatmap`` -> ``server/plot.py::plot_gene_heatmap`` -> ``core/plots/gene_heatmap.py::plot_gene_heatmap``
- ``modalysis plot dmr-dotplot`` -> ``cli/parsers/plot.py`` -> ``cli/handlers/plot.py`` -> ``client/plot.py::plot_dmr_dotplot`` -> ``server/plot.py::plot_dmr_dotplot`` -> ``core/plots/dmr_dotplot.py::plot_dmr_dotplot``
- ``modalysis plot common-genes-venn`` -> ``cli/parsers/plot.py`` -> ``cli/handlers/plot.py`` -> ``client/plot.py::plot_common_genes_venn`` -> ``server/plot.py::plot_common_genes_venn`` -> ``core/plots/common_genes_venn.py::plot_common_genes_venn``