---
name: "locuspocus"
section: "1"
platform: "linux"
package: "aegean"
version: "0.16.0+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/locuspocus"
---

# locuspocus(1)

calculate locus coordinates for the given gene annotation

## NAME

locuspocus - calculate locus coordinates for the given gene annotation

## SYNOPSIS

**locuspocus** \[*options*\] *gff3file1* \[*gff3file2 gff3file3* ...\]

## DESCRIPTION

Basic options:

- **-d**\|--debug

  print detailed debugging messages to terminal (standard error)

- **-h**\|--help

  print this help message and exit

- **-v**\|--version

  print version number and exit

-

  iLocus parsing:

- **-l**\|--delta: INT

  when parsing interval loci, use the following delta to extend gene loci and include potential regulatory regions; default is 500

- **-s**\|--skipends

  when enumerating interval loci, exclude unannotated (and presumably incomplete) iLoci at either end of the sequence

- **-e**\|--endsonly

  report only incomplete iLocus fragments at the unannotated ends of sequences (complement of **--skipends**)

- **-y**\|--skipiiloci

  do not report intergenic iLoci

-

  Refinement options:

- **-r**\|--refine

  by default genes are grouped in the same iLocus if they have any overlap; 'refine' mode allows for a more nuanced handling of overlapping genes

- **-c**\|--cds

  use CDS rather than UTRs for determining gene overlap; implies 'refine' mode

- **-m**\|--minoverlap: INT

  the minimum number of nucleotides two genes must overlap to be grouped in the same iLocus; default is 1

-

  Output options:

- **-n**\|--namefmt: STR

  provide a printf-style format string to override the default ID format for newly created loci; default is 'locus%lu' (locus1, locus2, etc) for loci and 'iLocus%lu' (iLocus1, iLocus2, etc) for interval loci; note the format string should include a single %lu specifier to be filled in with a long unsigned integer value

- **-i**\|--ilens: FILE

  create a file with the lengths of each intergenic iLocus

- **-g**\|--genemap: FILE

  print a mapping from each gene annotation to its corresponding locus to the given file

- **-o**\|--outfile: FILE

  name of file to which results will be written; default is terminal (standard output)

- **-T**\|--retainids

  retain original feature IDs from input files; conflicts will arise if input contains duplicated ID values

- **-t**\|--transmap: FILE

  print a mapping from each transcript annotation to its corresponding locus to the given file

- **-V**\|--verbose

  include all locus subfeatures (genes, RNAs, etc) in the GFF3 output; default includes only locus features

-

  Input options:

- **-f**\|--filter: TYPE

  comma-separated list of feature types to use in constructing loci/iLoci; default is 'gene'

- **-p**\|--parent: CT:PT

  if a feature of type $CT exists without a parent, create a parent for this feature with type $PT; for example, mRNA:gene will create a gene feature as a parent for any top-level mRNA feature; this option can be specified multiple times

- **-u**\|--pseudo

  correct erroneously labeled pseudogenes