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