# LocusPocus¶

## Introduction¶

LocusPocus is a program for computing interval loci (iLoci) from a provided set gene annotations. Each iLocus corresponds 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 a dash (-) is provided as the input filename). The only strict requirement is that the input must be valid GFF3, although users should be aware of the common pitfalls described on this page.

The use of ##sequence-region pragmas is optional, and many GFF3 files do not include them. LocusPocus uses this information when computing the location of iLoci at the ends of a sequence. Note that if these pragmas are not declared explicitly, iLoci will only be reported for sequence regions containing annotated features.

Users can override gene as the default feature of interest, replace it with one or more other 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 iLocus features themselves are reported, with attributes indicating the number of genes and transcripts in the locus. Invoking the –verbose option enables reporting of the gene features (and their subfeatures) as well.

## Running LocusPocus¶

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

locuspocus --help