homGeneMapping - create summary of gene homology

       An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.

                                                                                               HOMGENEMAPPING(1)

       AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

homGeneMapping takes a set of gene predictions of different genomes and a hal alignment of the genomes
       and prints a summary for each gene, e.g.

       •   how many of its exons/introns are in agreement with genes of other genomes

       •   how many of its exons/introns are supported by extrinsic evidence from any of the genomes

       •   a list of geneids of homologous genes

       homGeneMapping --noDupes --halLiftover_exec_dir=~/tools/progressiveCactus/submodules/hal/bin
       --gtfs=gtffilenames.tbl --halfile=msca.hal homGeneMapping --gtfs=gtffilenames.tbl --halfile=aln.hal
       --outdir=outdir --cpus=4

       homGeneMapping - create summary of gene homology

Mandatoryparameters--halfile=aln.hal
           input hal file

       --gtfs=gtffilenames.tbl
           a text file containing the locations of the input gene files and optionally the hints files (both in
           GTF format). The file is formatted as follows:

               name_of_genome_1  path/to/genefile/of/genome_1  path/to/hintsfile/of/genome_1
               name_of_genome_2  path/to/genefile/of/genome_2  path/to/hintsfile/of/genome_2
               ...
               name_of_genome_N  path/to/genefile/of/genome_N  path/to/hintsfile/of/genome_N

   Additionaloptions--cpus=N
           N is the number of CPUs to use (default: 1)

       --noDupes
           do not map between duplications in hal graph (default: off)

       --details
           print detailed output (default: off)

       --halLiftover_exec_dir=DIR
           Directory that contains the executable halLiftover If not specified it must be in $PATH environment
           variable.

       --unmapped
           print a GTF attribute with a list of all genomes, that are not aligned to the corresponding gene
           feature, e.g. hgm_unmapped \"1,4,5\"; (default; off)

       --tmpdir=DIR
           a temporary file directory that stores lifted over files (default 'tmp/' in current directory)

       --outdir=DIR
           file directory that stores output gene files (default: current directory)

       --printHomologs=FILE
           prints disjunct sets of homologous transcripts to FILE, e.g.

               # 0     dana
               # 1     dere
               # 2     dgri
               # 3     dmel
               # 4     dmoj
               # 5     dper
               (0, jg4139.t1) (0, jg4140.t1) (1, jg7797.t1) (2, jg3247.t1) (4, jg6720.t1) (5, jg313.t1)
               (1, jg14269.t1) (3, jg89.t1) (5, jg290.t1)
               ...
               Two transcripts are in the same set, if all their exons/introns are homologs and their are
               no additional exons/introns.
               This option requires the Boost C++ Library

       --dbaccess=db
           retrieve hints from an SQLite database. In order to set up a database and populate it with hints a
           separate tool 'load2sqlitedb' is provided. For more information, see the documentation in
           docs/RUNNING-AUGUSTUS-IN-CGP-MODE.md (DATABASE ACCESS / SQLite) in the Augustus package. If both a
           database and hint files in 'gtffilenames.tbl' are specified, hints are retrieved from both sources.

homGeneMapping [options] --gtfs=gffilenames.tbl --halfile=aln.hal