CLI Overview

cis-gs is the command-line counterpart of the GUI. Every workflow step has its own subcommand, plus a guided wizard that walks new users through the whole pipeline.

usage: cis-gs [-h] {wizard,fetch,extract,search,feed,coexpr,
                    kmeans,enrich-kegg,id-convert} ...

wizard         Step-by-step wizard (recommended for new users)
fetch          Download a genome + annotation from NCBI
extract        Extract promoter sequences from FASTA + GFF3
search         Scan promoters for motif occurrences
feed           Couple motif hits with an expression table
coexpr         Build a co-expression network
kmeans         K-means clustering with elbow / silhouette
enrich-kegg    KEGG over-representation analysis
id-convert     Convert gene IDs across namespaces (MyGene.info, batched)

Every subcommand accepts -i / --interactive for a step-by-step prompt.

Conveniences

  • Did-you-mean — mistype a command and Cis-GS suggests the closest match using difflib.SequenceMatcher.

  • Live KEGG dropdown in interactive mode (11 700+ organisms).

  • Live NCBI Taxonomy search in interactive mode.

  • Batched MyGene.info — 10 000 gene IDs convert in ~60 s instead of ~60 min.