[BioRuby] Detect error from Bio::Fetch

Yen-Ju Chen yjchenx at gmail.com
Thu Dec 13 05:22:36 UTC 2007


This is the script I run:

require 'bio'
serv = Bio::Fetch.new()
entry = serv.fetch('swissprot', 'not_existing_id')
swissprot = Bio::SwissProt.new(entry)
p swissprot.entry_name # <== Error raises here

The problem is that Bio.Fetch does not raise an exception or something
else to notify that it cannot find the entry in database. An error
shows up only at 'swissprot.entry_name'. It would be nice to detect
the error early on, either in Bio::Fetch.fetch() or
Bio::SwissProt.new().

Yen-Ju



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