DOKK / manpages / debian 10 / augustus / homGeneMapping.1.en
HOMGENEMAPPING(1)   HOMGENEMAPPING(1)

homGeneMapping - create summary of gene homology

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

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

--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

--cpus=N

N is the number of CPUs to use (default: 1)

--noDupes

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

--halLiftover_exec_dir=DIR

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

--tmpdir=DIR

a temporary file directory that stores lifted over files. (default 'tmp/' in current directory)

--outdir=DIR

file direcory 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

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

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

An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.