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locuspocus - calculate locus coordinates for the given gene annotation


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


Basic options:

print detailed debugging messages to terminal (standard error)

print this help message and exit

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

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

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

do not report intergenic iLoci

Refinement options:

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

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

-o|--outfile: FILE
name of file to which results will be written; default is terminal (standard

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

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

-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

correct erroneously labeled pseudogenes

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