locuspocus - calculate locus coordinates for the given gene
annotation
locuspocus [options] gff3file1 [gff3file2
gff3file3 ...]
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