# LocusPocus¶

## Introduction¶

LocusPocus is a program for computing interval loci (iLoci) from a provided set gene annotations. iLoci correspond to a single gene, a set of overlapping genes, or a space between genes. See this page for a description of iLoci as an organizational principle for genomics.

## Input¶

Input for LocusPocus is one or more files in GFF3 format (LocusPocus can also read from standard input if - is provided as the input filename). Aside from compliance to GFF3 syntax, the only requirement LocusPocus places on the input data is that gene features must be explicitly declared. Note: LocusPocus output may be more descriptive depending on whether additional features are described in the input, but the iLoci themselves depend only on gene features.

Alternatively, users can override gene as the default feature of interest, replace it with one or more feature types, and construct iLoci for these features in the same way.

## Output¶

LocusPocus computes the location of the iLoci from the given gene features and reports the iLocus locations in GFF3 format. By default, only the locus feature itself is reported, with attributes that indicate the number of genes in the locus (as well as gene children such as mRNA, tRNA, etc, if they are provided in the input). Invoking the –verbose option will additionally report all gene features (and their subfeatures) associated with the locus.

## Running LocusPocus¶

For a description of LocusPocus’ command-line interface, run the following command (after AEGeAn has been installed).

locuspocus --help