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