svr_split_fams < protein.families > without.multiple 2> with.cycles

Detect cases in which BBHs have led to cycles

Introduction

If you are constructing protein families and using comparisons that are BBHs, you often wish to avoid cases in which a single family has more than one gene/protein from a single genome. This little utility splits out the sets with multiple genes from a single genome, writes the removed entries to STDERR, and you can peruse them manually.

Output

The output consists of sets without cycles going to STDOUT and sets with cycles going to STDERR