[BioRuby] bioruby shell
Davide Rambaldi
davide.rambaldi at ifom-ieo-campus.it
Thu Sep 25 16:18:39 UTC 2008
Hello,
I have posted as a reply in another thread a small modification to
lib/bio/shell/plugin/entry.rb that resolve the demo problem (die
after trying to download a genbank from KeggAPI):
diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/
entry.rb
index 6d36fb5..0a45ecd 100644
--- a/lib/bio/shell/plugin/entry.rb
+++ b/lib/bio/shell/plugin/entry.rb
@@ -88,8 +88,16 @@ module Bio::Shell
# KEGG API at http://www.genome.jp/kegg/soap/
else
- puts "Retrieving entry from KEGG API (#{arg})"
entry = bget(arg)
+ if $?.exitstatus == 0 and str.length != 0
+ puts "Retrieving entry from KEGG API (#{arg})"
+ else
+ # efetch from NCBI
+ puts "Retrieving entry from NCBI (#{arg})"
+ require 'bio/io/ncbirest.rb'
+ fetch = Bio::NCBI::REST.efetch("AF237819",
{"db"=>"nuccore", "rettype"=>"gb"})
+ entry = fetch.to_s
+ end
end
end
I have some other ideas for the shell:
- adding a method to remove all saved objects
- making an help (at least for demo, ls and rm commands)
- adding an OptionParser
In general I want to propose some other simple modification to this
part of the bioruby library.
I am losing my time? there is another person on this?
or I can go on?
Many thanks for feedback
P.S: my simple BLAT application blatanalyzer is now accessible via
svn at
svn checkout svn://rubyforge.org/var/svn/blatanalyzer/trunk
any feedback is really appreciated
thanks again
Davide Rambaldi,
Bioinformatics PhD student.
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Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi
(homepage)
[i] http://www.semm.it (PhD school)
[i] http://www.btbs.unimib.it/ (Master)
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