Feature: Parse MAF files In order to extract information from a MAF file I want to read it and pull out information

Scenario: Read MAF header Given MAF data: """ ##maf version=1 scoring=humor.v4 # humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet25/chr22.maf /cluster/data/hg15/bed/blastz.rn3/axtNet25/chr22.maf

a score=0.128
s human_hoxa 100  8 + 100257 ACA-TTACT
s horse_hoxa 120  9 -  98892 ACAATTGCT
s fugu_hoxa   88  7  + 90788 ACA--TGCT
"""
When I open it with a MAF reader
Then the MAF version should be "1"
And the scoring scheme should be "humor.v4"
# third line a continuation
And the alignment parameters should be "humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet25/chr22.maf /cluster/data/hg15/bed/blastz.rn3/axtNet25/chr22.maf" 

Scenario: Read alignment block Given MAF data: """ ##maf version=1 scoring=humor.v4 # humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf # /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf

a score=0.128
s human_hoxa 100  8 + 100257 ACA-TTACT
s horse_hoxa 120  9 -  98892 ACAATTGCT
s fugu_hoxa   88  7  + 90788 ACA--TGCT
"""
When I open it with a MAF reader
Then an alignment block can be obtained
And the alignment block has 3 sequences
And sequence 0 has source "human_hoxa"
And sequence 0 has start 100
And sequence 0 has size 8
And sequence 0 has strand :+
And sequence 0 has source size 100257
And sequence 0 has text "ACA-TTACT"
And sequence 1 has strand :-

Scenario: Read alignment block, folded to upper case Given MAF data: """ ##maf version=1 scoring=humor.v4 # humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf # /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf

a score=0.128
s human_hoxa 100  8 + 100257 aca-ttact
s horse_hoxa 120  9 -  98892 acaattgct
s fugu_hoxa   88  7  + 90788 aca--tgct
"""
When I enable the :upcase parser option
And I open it with a MAF reader
Then an alignment block can be obtained
And the alignment block has 3 sequences
And sequence 0 has text "ACA-TTACT"