The Wizard

cis-gs wizard

Launches an interactive walkthrough of every Cis-GS workflow. The wizard:

  • Guides you through each step with numbered prompts and sensible defaults.

  • Accepts free-form paths, IDs, and parameters with inline validation.

  • Mirrors the GUI experience for headless servers and HPC nodes.

You can launch a specific workflow directly:

cis-gs wizard                 # top-level menu - pick a workflow
cis-gs wizard kegg            # KEGG enrichment (live organism picker)
cis-gs wizard id-convert      # Gene-ID conversion
cis-gs wizard feed            # Expression feeding
cis-gs wizard coexpr          # Co-expression network
cis-gs wizard kmeans          # K-means clustering
cis-gs wizard fetch           # NCBI genome fetch
cis-gs wizard extract         # Promoter extraction (Step 1)
cis-gs wizard search          # Motif search (Step 2)
cis-gs wizard batch           # Multi-species batch (Steps 1+2)

Available workflows

Workflow

Description

kegg

KEGG pathway over-representation with live organism search (~11,700 entries)

id-convert

Translate gene IDs between LOC, Ensembl, Entrez, and symbol formats

feed

Filter an expression matrix to genes with motif hits

coexpr

Build a co-expression network and detect Louvain modules

kmeans

K-means clustering with optional elbow-method auto-k

fetch

Download genome FASTA + GFF3 from NCBI Assembly by organism name

extract

Extract upstream promoter sequences from a genome FASTA + GFF3

search

Scan promoters for IUPAC motif hits

batch

Run extraction + search for multiple species from a single manifest file

Multi-species batch wizard

The batch wizard (new in v1.3.0) automates Steps 1 and 2 for any number of species in a single run. Prepare a tab-separated manifest file:

# species_name<TAB>fasta_path<TAB>gff3_path[<TAB>upstream_bp]
O. sativa      /data/rice.fa        /data/rice.gff3        2000
A. hypogaea    /data/peanut.fa      /data/peanut.gff3      2000
M. truncatula  /data/medicago.fa    /data/medicago.gff3    2000

Then run:

cis-gs wizard batch
# or non-interactively:
cis-gs batch species.tsv --motifs-file motifs.txt -o batch_out/

Output files written to the output directory:

  • <species>_promoters.fa - extracted promoters per species

  • <species>_hits.csv - motif hits per species

  • batch_hits.csv - combined hits for all species (species column added)