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locuspocus - Online in the Cloud

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This is the command locuspocus that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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