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Contents
require 'spec_helper'
require 'generators/templates/blast_db'
describe "Quorum::FetchTools::BlastDb" do
describe "#execute_blast_db_cmd" do
before(:each) do
# Set the args as though we executed bin/fetch
@args = {
:fetch_tool => "blastdbcmd",
:blast_hit_id => nil,
:blast_hit_display_id => nil,
:blast_algo => nil,
:fetch_database_names => "test",
:log_directory => File.expand_path(
"../../dummy/quorum/log", __FILE__
),
:tmp_directory => File.expand_path(
"../../dummy/quorum/tmp", __FILE__
),
:fetch_database => File.expand_path(
"../../dummy/quorum/blastdb", __FILE__
)
}
end
it "executes blastdbcmd for blastn and returns correct sequence" do
@args[:blast_hit_id] = "gnl|BL_ORD_ID|0"
@args[:blast_hit_display_id] = "TOG900080"
@args[:blast_algo] = "blastn"
seqs = File.readlines(
File.expand_path("../../data/nucl_seqs.txt", __FILE__)
)
seqs[0].gsub!(">", "")
seqs.insert(0, ">" + @args[:blast_hit_id] + " ")
# Sequence #execute_blast_db_cmd should return.
seq = seqs.slice(0,3).join("").gsub("\n", "")
fetch = Quorum::FetchTools::BlastDb.new(@args)
lambda {
output = capture(:stdout) {
fetch.execute_blast_db_cmd
}
output.gsub("\n", "").should eq(seq)
}.should_not raise_error
end
it "returns error message if filtered sequence.length != 1" do
@args[:blast_hit_id] = "null"
@args[:blast_hit_display_id] = "null"
@args[:blast_algo] = "blastp"
fetch = Quorum::FetchTools::BlastDb.new(@args)
lambda {
output = capture(:stdout) {
fetch.execute_blast_db_cmd
}
output.should eq("An error occurred while processing your request.")
}.should_not raise_error
end
end
end
Version data entries
6 entries across 6 versions & 1 rubygems