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.

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

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

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

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