'\" t
.\"     Title: homgenemapping
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "HOMGENEMAPPING" "1" "" "\ \&" "\ \&"
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.SH "NAME"
homGeneMapping \- create summary of gene homology
.SH "SYNOPSIS"
.sp
\fBhomGeneMapping\fP [options] \-\-gtfs=gffilenames.tbl \-\-halfile=aln.hal
.SH "DESCRIPTION"
.sp
\fBhomGeneMapping\fP 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.
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
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how many of its exons/introns are in agreement with genes of other genomes
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
how many of its exons/introns are supported by extrinsic evidence from any of the genomes
.RE
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.RS 4
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\h'-04'\(bu\h'+03'\c
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a list of geneids of homologous genes
.RE
.SH "OPTIONS"
.SS "Mandatory parameters"
.sp
\fB\-\-halfile=aln.hal\fP
.RS 4
input hal file
.RE
.sp
\fB\-\-gtfs=gtffilenames.tbl\fP
.RS 4
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:
.sp
.if n .RS 4
.nf
.fam C
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
.fam
.fi
.if n .RE
.RE
.SS "Additional options"
.sp
\fB\-\-cpus=N\fP
.RS 4
N is the number of CPUs to use (default: 1)
.RE
.sp
\fB\-\-noDupes\fP
.RS 4
do not map between duplications in hal graph (default: off)
.RE
.sp
\fB\-\-details\fP
.RS 4
print detailed output (default: off)
.RE
.sp
\fB\-\-halLiftover_exec_dir=DIR\fP
.RS 4
Directory that contains the executable halLiftover
If not specified it must be in $PATH environment variable.
.RE
.sp
\fB\-\-unmapped\fP
.RS 4
print a GTF attribute with a list of all genomes, that are not aligned to the
corresponding gene feature, e.g. hgm_unmapped \(rs"1,4,5\(rs"; (default; off)
.RE
.sp
\fB\-\-tmpdir=DIR\fP
.RS 4
a temporary file directory that stores lifted over files (default \*(Aqtmp/\*(Aq in current directory)
.RE
.sp
\fB\-\-outdir=DIR\fP
.RS 4
file directory that stores output gene files (default: current directory)
.RE
.sp
\fB\-\-printHomologs=FILE\fP
.RS 4
prints disjunct sets of homologous transcripts to FILE, e.g.
.sp
.if n .RS 4
.nf
.fam C
# 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
.fam
.fi
.if n .RE
.RE
.sp
\fB\-\-dbaccess=db\fP
.RS 4
retrieve hints from an SQLite database. In order to set up a database and populate it with hints
a separate tool \*(Aqload2sqlitedb\*(Aq 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 \*(Aqgtffilenames.tbl\*(Aq
are specified, hints are retrieved from both sources.
.RE
.SH "EXAMPLE"
.sp
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
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
.SH "ADDITIONAL DOCUMENTATION"
.sp
An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.