Sha256: 8542f657817ad4a5e9818cb290b6768a248481a56f6e4df02197a42fa166bf14
Contents?: true
Size: 1.56 KB
Versions: 11
Compression:
Stored size: 1.56 KB
Contents
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 :-
Version data entries
11 entries across 11 versions & 1 rubygems