Command Reference

cis-gs fetch

cis-gs fetch --organism "Arabidopsis thaliana" --out ./refs/

Searches NCBI Assembly, picks the latest RefSeq, downloads FASTA + GFF3.

cis-gs extract

cis-gs extract --fasta genome.fa --gff annot.gff3 \
               --upstream 2000 [--avoid-overlap] --out promoters.fa

cis-gs search

cis-gs search --promoters promoters.fa --motifs motifs.meme \
              [--allow-overlap] [--rc] --out hits.csv

cis-gs batch

cis-gs batch species.tsv --motifs-file motifs.txt
cis-gs batch species.tsv --motifs-file motifs.txt -o results/ --upstream 1500

Runs promoter extraction (Step 1) and motif search (Step 2) for every species listed in a tab-separated manifest file, then writes per-species hit CSVs and a combined batch_hits.csv with an extra species column.

Manifest format (tab-separated, one species per line):

# species_name<TAB>fasta<TAB>gff3[<TAB>upstream_bp]
O. sativa     /data/rice.fa      /data/rice.gff3      2000
A. hypogaea   /data/peanut.fa    /data/peanut.gff3    2000

Options:

--motifs-file FILE Motifs file - NAME<TAB>IUPAC_PATTERN per line (required)
-o / --out DIR Output directory (default: batch_out/)
--upstream BP Default upstream length when not specified per row (default: 2000)

Interactive: cis-gs wizard batch

cis-gs logo

cis-gs logo hits.csv
cis-gs logo hits.csv -o ./logos --scale probability
cis-gs logo hits.csv --length 9

Generates sequence logo images (PNG) from the matched_seq column of a motif hit CSV produced by cis-gs search. One PNG is written per motif: logos/logo_<motif_name>.png.

Options:

-o / --outdir DIR Output directory (default: logos/)
--scale y-axis scale: bits (information content, default) or probability
--length N Only include sequences of exactly N bp (useful when a motif has length-variable hits)

cis-gs feed

cis-gs feed --hits hits.csv --expression expr.csv \
            [--mapping mapping.csv] [--gff3 annot.gff3] \
            --out matched.csv

cis-gs coexpr

cis-gs coexpr --expression expr.csv \
              [--method pearson|spearman] \
              [--soft-power 6] \
              [--module-method louvain|hierarchical] \
              --out network.gexf

cis-gs kmeans

cis-gs kmeans --expression expr.csv -k 6 \
              [--seed 42] [--elbow] --out clusters/

cis-gs enrich-kegg

cis-gs enrich-kegg --organism ath --genes top_module.txt \
                   [--background bg.txt] \
                   [--min-overlap 2] [--min-set-size 5] \
                   --out kegg.csv

cis-gs id-convert

cis-gs id-convert --species human --target ensembl \
                  --infile genes.txt --out ensembl.csv

Routes through MyGene.info via a batched POST (chunks of 1 000 IDs) with a live progress bar. ~60× faster than the legacy per-ID GET.