locuspocus - Online in the Cloud

PROGRAM:

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

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