[BioRuby] More Bl2seq questions
Trevor Wennblom
trevor at corevx.com
Thu Sep 8 18:05:13 EDT 2005
Another question regarding Bl2seq.
This works:
Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, filename_bl2seq_output)
do |ff|
ff.each do |rep|
rep.iterations.each do |itr|
itr.hits.each do |hit|
a = hit.identity
end
end
end
end
But this doesn't:
Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, filename_bl2seq_output)
do |ff|
ff.each do |rep|
rep.iterations.each do |itr|
itr.hits.each do |hit|
a = hit.percent_identity
end
end
end
end
To make it work I have to go down to the HSP level:
Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, filename_bl2seq_output)
do |ff|
ff.each do |rep|
rep.iterations.each do |itr|
itr.hits.each do |hit|
hit.hsps.each do |hsp|
a = hsp.percent_identity
end
end
end
end
end
Shouldn't we be able to see percent_identity, percent_positive,
positive, etc. on the hit level?
Trevor
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