Contents

require_relative '../spec_helper'
require_relative '../../lib/bioinform/parsers/string_fantom_parser'

module Bioinform
  describe StringFantomParser do
    describe '#split_on_motifs' do
      it 'should be able to parse several motifs' do
        input = "
//
NA  motif_1
P0	A	C	G	T
P1	0 1	2	3
P2	4 5	6	7
//
//
NA  motif_2
P0	A	C	G	T
P1  1 2 3 4
P2  5 6 7 8
P3  9 10 11 12
//
NA  motif_3
P0	A	C	G	T
P1	2 3	4 5
P2	6 7 8 9"
        StringFantomParser.split_on_motifs(input).should == [ Fabricate(:pm_1), Fabricate(:pm_2), Fabricate(:pm_3) ]
      end
    end

    good_cases = {
      'string in Fantom-format' => {input: "
        NA  PM_name
        P0	A	C	G	T
        P1	1	2	3 4
        P2	5	6	7 8",
        result: Fabricate(:pm)
      },

      'motif with additional rows' => {input: "
        NA  PM_name
        P0	A C G T S P
        P1	1 2 3 4 5 10
        P2	5 6 7 8 5 11",
        result: Fabricate(:pm)
      },
      
      'string with more than 10 positions(2-digit row numbers)' => {input: "
        NA  PM_name
        P0	A	C	G	T
        P1	1	2	3	4
        P2	5	6	7	8
        P3	1	2	3	4
        P4	5	6	7	8
        P5	1	2	3	4
        P6	5	6	7	8
        P7	1	2	3	4
        P8	5	6	7	8
        P9	1	2	3	4
        P10	5	6	7	8
        P11	1	2	3	4
        P12	5	6	7	8",
        result: Fabricate(:pm, matrix: [[1,2,3,4],[5,6,7,8]] * 6 )
      }
    }

    bad_cases = { }

    parser_specs(StringFantomParser, good_cases, bad_cases)
  end
end

Version data entries

5 entries across 5 versions & 1 rubygems

Version	Path
bioinform-0.1.12	spec/parsers/string_fantom_parser_spec.rb
bioinform-0.1.11	spec/parsers/string_fantom_parser_spec.rb
bioinform-0.1.10	spec/parsers/string_fantom_parser_spec.rb
bioinform-0.1.9	spec/parsers/string_fantom_parser_spec.rb
bioinform-0.1.8	spec/parsers/string_fantom_parser_spec.rb