File: homGeneMapping.1.adoc

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# homGeneMapping(1)

## NAME

homGeneMapping - create summary of gene homology

## SYNOPSIS

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

## DESCRIPTION

*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

## OPTIONS

### Mandatory parameters

*--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

### Additional options

*--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 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

## EXAMPLE

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

## AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. K├Ânig, L. Gerischer and L. Romoth.

## ADDITIONAL DOCUMENTATION

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