pangyplot cytoband

Generate a dummy cytoband for an organism with no cytogenetic data.

SYNOPSIS

pangyplot cytoband --fai FILE [OPTION]…

DESCRIPTION

Generates a dummy cytoband from a reference FASTA index (.fai), so that organisms with no cytoband data can still be visualized in PangyPlot. Each chromosome is drawn as a single bar spanning its length.

Two files are written into --out-dir:

{genome}.cytoBand.txt — the cytoband file
{genome}.canonical.txt — the canonical chromosome list, one name per line

Point CYTOBAND_PATH and CANONICAL_PATH at them and set ORGANISM=custom (see Dotenv Setup). The command prints the exact lines to add to your .env.

Note

Sequences shorter than --min-length (1,000,000 bp by default) are left out, since a .fai usually lists many unplaced scaffolds. The command reports what it kept and what it dropped.

OPTIONS

MANDATORY OPTIONS

--fai FILE

Path to a FASTA .fai index. A plain name<TAB>length TSV also works.

OUTPUT OPTIONS

--out-dir DIR

Directory to write the two files into (default: current directory).

--genome STRING

Genome name used for the output filenames (default: derived from --fai).

SEQUENCE SELECTION OPTIONS

--min-length INT

Drop sequences shorter than this many bp (default: 1000000). Use 0 to keep every sequence.

--chromosomes STRING

Comma-separated list of sequences to keep, in this order. Overrides --min-length and --pattern.

--pattern REGEX

Keep only sequences whose name matches this regular expression, e.g. ^chr.

BANDING OPTIONS

--band-size INT

Subdivide each chromosome into shaded bands of this many bp, as a coordinate ruler. Default: a single bar per chromosome.

--num-bands INT

Subdivide each chromosome into this many bands, as an alternative to --band-size.

CONVENIENCE OPTIONS

--force

Overwrite existing files without prompting.

EXAMPLES

Index the reference FASTA, then generate the cytoband:

samtools faidx myorganism.fa
pangyplot cytoband --fai myorganism.fa.fai --out-dir cytoband/ --genome myOrg

Keep only the named chromosomes, in that order:

pangyplot cytoband --fai myorganism.fa.fai \
    --chromosomes chr1,chr2,chr3,chrX

Subdivide into 1 Mb bands, and keep every sequence including short scaffolds:

pangyplot cytoband --fai myorganism.fa.fai \
    --band-size 1000000 --min-length 0