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Versions: 9
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Contents
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"
Version data entries
9 entries across 9 versions & 1 rubygems