shuffleGff

shuffleGff -- a Perl script to shuffle genomic features leaving the gene models intact

Usage

shuffleRanges.pl -chromsizes chromsizes.txt -excludes xclude.gff3 -out shuffled.gff3 -minlength 1000 -progress -verbose input.gff3

Dependencies

• Set::IntervalTree
• BioPerl

Options

• -chromsizes file.txt: a tab separated file with two columns: chromosome of landmark name, length. This file will be used to draw regions.
• -excludes file.gff3: a .gff3 formatted file with regions to avoid when placing features (optional)
• -out shuffled.gff3: output file (default shuffled.gff3)
• -minlength: minimal length of chromosome or landmark to draw from (default: 1000) to avoid redraws
• -progress: display a progress counter
• -verbose: more annoying output

Bugs

• Many