list_genomes
Martin Asser Hansen edited this page Oct 2, 2015
·
5 revisions
Genomes are formatted with format_genome.
list_genomes [options]
[-? | --help] # Print full usage description.
[-v | --verbose] # Verbose output.
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/
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
list_genomes is part of the Biopieces framework.