Feature: Convert MAF file to FASTA In order to use multiple alignment data with other tools I want to read a Multiple Alignment Format (MAF) file and write out its data as FASTA

Scenario: Convert simple MAF file Given a MAF source file "t1.maf" When I select FASTA output And I open it with a MAF reader And process the file Then the output should match "t1.fasta"

Scenario: Convert simple MAF data 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


a score=0.071
s human_unc 9077 8 + 10998 ACAGTATT
# Comment
s horse_unc 4555 6 -  5099 ACA--ATT
s fugu_unc  4000 4 +  4038 AC----TT
"""
When I select FASTA output
And I open it with a MAF reader
And process the file
Then the output should be:
"""
>human_hoxa:100-108
ACA-TTACT
>horse_hoxa:120-129
ACAATTGCT
>fugu_hoxa:88-95
ACA--TGCT
>human_unc:9077-9085
ACAGTATT
>horse_unc:4555-4561
ACA--ATT
>fugu_unc:4000-4004
AC----TT

"""

@no_jruby Scenario: Convert MAF to FASTA with CLI tool Given test files: | mm8_chr7_tiny.maf | When I run maf_to_fasta mm8_chr7_tiny.maf mm8_chr7_tiny.fa Then it should pass with: """ """ And the file "mm8_chr7_tiny.fa" should contain ">rn4.chr1:136011785-136011819"