Provided by: aegean_0.15.2+dfsg-2_amd64 bug


       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