.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH LOCUSPOCUS "1" "January 2016" "locuspocus 0.15.1" "User Commands"
.SH NAME
locuspocus \- calculate locus coordinates for the given gene annotation
.SH SYNOPSIS
.B locuspocus
[\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 gff3file3 \/\fR...]
.SH DESCRIPTION
Basic options:
.TP
\fB\-d\fR|\-\-debug
print detailed debugging messages to terminal
(standard error)
.TP
\fB\-h\fR|\-\-help
print this help message and exit
.TP
\fB\-v\fR|\-\-version
print version number and exit
.IP
iLocus parsing:
.TP
\fB\-l\fR|\-\-delta: INT
when parsing interval loci, use the following
delta to extend gene loci and include potential
regulatory regions; default is 500
.TP
\fB\-s\fR|\-\-skipends
when enumerating interval loci, exclude
unannotated (and presumably incomplete) iLoci at
either end of the sequence
.TP
\fB\-e\fR|\-\-endsonly
report only incomplete iLocus fragments at the
unannotated ends of sequences (complement of
\fB\-\-skipends\fR)
.TP
\fB\-y\fR|\-\-skipiiloci
do not report intergenic iLoci
.IP
Refinement options:
.TP
\fB\-r\fR|\-\-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
.TP
\fB\-c\fR|\-\-cds
use CDS rather than UTRs for determining gene
overlap; implies 'refine' mode
.TP
\fB\-m\fR|\-\-minoverlap: INT
the minimum number of nucleotides two genes must
overlap to be grouped in the same iLocus; default
is 1
.IP
Output options:
.TP
\fB\-n\fR|\-\-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
.TP
\fB\-i\fR|\-\-ilens: FILE
create a file with the lengths of each intergenic
iLocus
.TP
\fB\-g\fR|\-\-genemap: FILE
print a mapping from each gene annotation to its
corresponding locus to the given file
.TP
\fB\-o\fR|\-\-outfile: FILE
name of file to which results will be written;
default is terminal (standard output)
.TP
\fB\-T\fR|\-\-retainids
retain original feature IDs from input files;
conflicts will arise if input contains duplicated
ID values
.TP
\fB\-t\fR|\-\-transmap: FILE
print a mapping from each transcript annotation
to its corresponding locus to the given file
.TP
\fB\-V\fR|\-\-verbose
include all locus subfeatures (genes, RNAs, etc)
in the GFF3 output; default includes only locus
features
.IP
Input options:
.TP
\fB\-f\fR|\-\-filter: TYPE
comma\-separated list of feature types to use in
constructing loci/iLoci; default is 'gene'
.TP
\fB\-p\fR|\-\-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
.TP
\fB\-u\fR|\-\-pseudo
correct erroneously labeled pseudogenes