Sha256: d8e27d1b3b9c4cc057a23423af865de85ee3e9435f7910d02ffe3c01cebb62da
Contents?: true
Size: 969 Bytes
Versions: 11
Compression:
Stored size: 969 Bytes
Contents
Given /^chromosome reference sequence:$/ do |string|
sio = StringIO.new(string)
@refseq = Bio::MAF::FASTARangeReader.new(sio)
end
When /^tile ([^:\s]+):(\d+)-(\d+)( with the chromosome reference)?$/ do |seq, i_start, i_end, ref_p|
@tiler = Bio::MAF::Tiler.new
@tiler.index = @idx
@tiler.parser = @parser
@tiler.reference = @refseq if ref_p
@tiler.interval = Bio::GenomicInterval.zero_based(seq,
i_start.to_i,
i_end.to_i)
end
When /^tile with species \[(.+?)\]$/ do |species_text|
@tiler.species = species_text.split(/,\s*/)
end
When /^map species (\S+) as (\S+)$/ do |sp1, sp2|
@tiler.species_map[sp1] = sp2
end
When /^write the tiled data as FASTA$/ do
@dst = Tempfile.new(["cuke", ".fa"])
@tiler.write_fasta(@dst)
end
Then /^the FASTA data obtained should be:$/ do |string|
@dst.seek(0)
@dst.read.rstrip.should == string.rstrip
end
Version data entries
11 entries across 11 versions & 1 rubygems