[BioRuby-cvs] bioruby/lib/bio/io ensembl.rb,1.6,1.7
Mitsuteru C. Nakao
nakao at dev.open-bio.org
Thu Mar 29 05:24:30 UTC 2007
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv9701/lib/bio/io
Modified Files:
ensembl.rb
Log Message:
* Fixed a bug in exportview argument parsing.
Index: ensembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ensembl.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** ensembl.rb 28 Mar 2007 12:31:48 -0000 1.6
--- ensembl.rb 29 Mar 2007 05:24:27 -0000 1.7
***************
*** 65,70 ****
--- 65,72 ----
ENSEMBL_URL = 'http://www.ensembl.org'
+ # Server URL (ex. 'http://www.ensembl.org')
attr_reader :server
+ # Organism name. (ex. 'Homo_sapiens').
attr_reader :organism
***************
*** 138,157 ****
#
def exportview(*args)
- if args.first.class == Hash
- options = args.first
- else
- options = {
- :seq_region_name => args[0],
- :anchor1 => args[1],
- :anchor2 => args[2],
- }
- case args.size
- when 3 then
- options.update({:format => 'fasta'})
- when 4 then
- options.update({:format => 'gff', :options => args[3]})
- end
- end
-
defaults = {
:type1 => 'bp',
--- 140,143 ----
***************
*** 167,170 ****
--- 153,170 ----
}
+ if args.first.class == Hash
+ options = args.first
+ options.update({:format => 'gff'}) if options[:options] and options[:format] != 'fasta'
+ else
+ options = {
+ :seq_region_name => args[0],
+ :anchor1 => args[1],
+ :anchor2 => args[2],
+ }
+ if args.size >= 4
+ options.update({:format => 'gff', :options => args[3]})
+ end
+ end
+
params = defaults.update(options)
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