list_genomes

Biopiece: list_genomes

Description

Genomes are formatted with format_genome.

Usage

list_genomes [options]

Options

[-? | --help]     #  Print full usage description.
[-v | --verbose]  #  Verbose output.

Examples

To list available genomes and genome indexes of various types use list_genomes:

list_genomes

Genome  blast   blat    fasta   phastcons       vmatch
ara1    yes     yes     yes     no      yes
ce4     yes     no      yes     no      yes
danRer5 yes     no      yes     no      no
dm2     no      no      yes     no      no
dm3     yes     no      yes     yes     yes
dp4     no      no      yes     no      no
droAna3 no      no      yes     no      no
droEre2 no      no      yes     no      no
droGri2 no      no      yes     no      no
droMoj3 no      no      yes     no      no
droPer1 no      no      yes     no      no
droSec1 no      no      yes     no      no
droSim1 no      no      yes     no      no
droVir3 no      no      yes     no      no
droWil1 no      no      yes     no      no
droYak2 no      no      yes     no      no
galGal3 yes     no      yes     no      yes
hg18    yes     no      yes     yes     yes
mm8     no      no      yes     no      no
mm9     yes     no      yes     no      yes
sacCer1 yes     no      yes     no      yes
sacPom1 yes     no      yes     no      yes
tetNig1 no      no      yes     no      no

This information is based on the existence of relevant directories found in the BP_DATA directory tree:

BP_DATA/
  +-- genomes/
      +-- ara1/
      |   +-- blast/
      |   +-- blat/
      |   +-- fasta/
      |   +-- vmatch/
      +-- ce4/
      |   +-- blast/
      |   +-- fasta/
      |   +-- vmatch/
      +-- danRer5/
      |   +-- blast/
      |   +-- fasta/
      +-- dm2/
      |   +-- fasta/
      +-- dm3/
      |   +-- blast/
      |   +-- fasta/
      |   +-- phastcons/
      |   +-- vmatch/
      +-- dp4/
      |   +-- fasta/
      +-- droAna3/
      |   +-- fasta/
      +-- droEre2/
      |   +-- fasta/
      +-- droGri2/
      |   +-- fasta/
      +-- droMoj3/
      |   +-- fasta/
      +-- droPer1/
      |   +-- fasta/
      +-- droSec1/
      |   +-- fasta/
      +-- droSim1/
      |   +-- fasta/
      +-- droVir3/
      |   +-- fasta/
      +-- droWil1/
      |   +-- fasta/
      +-- droYak2/
      |   +-- fasta/
      +-- galGal3/
      |   +-- blast/
      |   +-- fasta/
      |   +-- vmatch/
      +-- hg18/
      |   +-- blast/
      |   +-- fasta/
      |   +-- phastcons/
      |   +-- vmatch/
      +-- mm8/
      |   +-- fasta/
      +-- mm9/
      |   +-- blast/
      |   +-- fasta/
      |   +-- vmatch/
      +-- sacCer1/
      |   +-- blast/
      |   +-- fasta/
      |   +-- vmatch/
      +-- sacPom1/
      |   +-- blast/
      |   +-- fasta/
      |   +-- vmatch/
      +-- tetNig1/
          +-- fasta/

See also

format_genome

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

mail@maasha.dk

August 2007

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

list_genomes is part of the Biopieces framework.

http://www.biopieces.org