Man page - homgenemapping(1)

Packages contas this manual

Manual

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)

--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 --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

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/doc/augustus/README.md.gz.