Blast is not a Module (Type Error) about blastxmlparser HOT 5 CLOSED

This sounds like a name space collision with bioruby and not a bug in blastxmlparser. Can you provide a code example? Thanks!

from blastxmlparser.

sample code:

#!/usr/bin/env ruby
require 'bio'
require 'bio-blastxmlparser'

all_hits = Array.new
blastfile = 'moore_metal_abc.blastxml'
  n = Bio::Blast::XmlIterator.new(blastfile).to_enum
  n.each do | iter |
    iter.each do | hit |
      all_hits << hit.hit_def
    end
  end

unique_hits = all_hits.uniq
print "Found #{unique_hits.count} unique hits from the #{all_hits.count} total hits\n"

db_fasta = '/home/shane/Documents/sequence_data/CAM_PROJ_MarineMicrobes/CAM_PROJ_MarineMicrobes_peptides_shortdef.fasta'
File.open('moore_abc_uniq_seqs.fasta', 'w') do |f|
  Bio::FlatFile.auto(db_fasta).each do | item |
    unique_hits.each do |seq|
        if seq == item.definition
          new_seq = Bio::FastaFormat.new('> '+item.definition+"\n"+item.data)
          f.puts new_seq
        end
      end
    end
  end

error received:

/usr/lib/ruby/gems/1.9.1/gems/bio-blastxmlparser-1.1.0/lib/bio/db/blast/xmliterator.rb:4:in <module:Bio>': Blast is not a module (TypeError) from /usr/lib/ruby/gems/1.9.1/gems/bio-blastxmlparser-1.1.0/lib/bio/db/blast/xmliterator.rb:3:in<top (required)>'
from /usr/local/lib/site_ruby/1.9.1/rubygems/custom_require.rb:36:in require' from /usr/local/lib/site_ruby/1.9.1/rubygems/custom_require.rb:36:inrequire'
from /usr/lib/ruby/gems/1.9.1/gems/bio-blastxmlparser-1.1.0/lib/bio-blastxmlparser.rb:19:in <top (required)>' from /usr/local/lib/site_ruby/1.9.1/rubygems/custom_require.rb:60:inrequire'
from /usr/local/lib/site_ruby/1.9.1/rubygems/custom_require.rb:60:in rescue in require' from /usr/local/lib/site_ruby/1.9.1/rubygems/custom_require.rb:35:inrequire'
from get_my_seqs.rb:3:in `

Thanks!!

from blastxmlparser.

I'll check what happened on the BioRuby side.

from blastxmlparser.

BioRuby has

module Bio
class Blast

The BlastXMLParser has

module Bio
module Blast

indeed, this is wrong. I should have named the surrounding Bio module something else. No reason to share that name space.

from blastxmlparser.

Version 1.1.1 has a fix in the form of changing Bio::Blast to Bio::BlastXMLParser name space.

from blastxmlparser.