Convert MAF to FASTA

Question

[tim.ivanov.92]

I've obtained multiple MAF files through UCSC. And i really want to be able to convert them into fasta files. Is there a tool for it? I found this github https://github.com/dentearl/mafTools/ which has mafToFastaStitcher tool, but the description says that it requires complete fasta records to work, which is an extra step and can in theory be avoided, if i understand it right.

But if it cannot - how can i get complete fasta records for my MAFs through UCSC?

for example:

##maf version=1 scoring=blastz
a score=1027970.000000
s dm6.chr2R              21257296 172 + 25286936 GAC--TGGACTGC---ATCAGATAGC---ATTAAATTGCTGGTCACTCG--------------CAATCAGCGAAAACAAGC--GAAAC-TGAATGGAGCAAA----CAAAGAGCAGTTATTGCGGGCAATC-----ATTAGTGATACAAATCGCCG--------AAACAATTCCCC---GGAGAT--------CTGGAACCTAATCAG-----------------GACA---------------------------------------------------------GTCCATG------A-----------------------------CCACA
s droSim1.chr2R          15795742 174 + 19596830 GACTGTGGCTTGG---ATCAGATAGT---ATTAAATTGCTGGTCACTCG--------------CAATCAGCGAAAACAAGC--GAAAC-TGAATGGAGCAAA----CAAAGAGCAGTTATTGCGGGCAATC-----ATTAGTGATACAAATCGCCG--------CAGCAACTCCCC---GGAGAT--------CTGGAACCTAATCAG-----------------GACA---------------------------------------------------------GTCCATG------A-----------------------------CCACA
i droSim1.chr2R          C 0 C 0
s droSec1.super_9          474992 172 +  3197100 GAC--TGGACTGG---ATCAGATAGT---ATTAAATTGCTGGTCACTCG--------------CAATCAGCGAAAACAAGC--GAAAC-TGAATGGAGCAAA----CAAAGAGCAGTTATTGCGGGCAATC-----ATTAGTGATACAAATCGCGG--------CAGCAATTCCCC---GGAGAT--------CTGGAACCTAATCAG-----------------GACA---------------------------------------------------------GTCCATG------A-----------------------------CCACA
i droSec1.super_9        C 0 C 0
s droYak3.chr2R           9094987 172 - 21139217 GAC---CGACTGG---ATCAGATAGT---ATTAAATTGCTGGTCACTCG--------------CAATCAGCGAAAACAAGC--GAAAC-TGAATGGAGCAAA----CAAAGGGCAGTTATTGCGGGCAATC-----ATTAGTGATACAAATCGCCG--------CAGCAATTCCCC---GGAGAT--------CTGAAACCTAATCAG-----------------GACA--------------------------------------------------------CAACCATG------A-----------------------------CCACA

How can i automatically download complete record of droSec1.super_9? I think there should be a way to do it

[GenoMax]

MAF to Fasta or XMFA - how does it work?
Need A Unix Script For The Galaxy Tool: Maf To Fasta (Version 1.0.1)

[tim.ivanov.92]

Thank you for the second link - i'll look into it

Do you mb know how to get complete UCSC fasta records by droSec1.super_9? I think i will need it anyway later

Answer 1

[kloetzl]

I am not sure what you want to achieve, but this extracts the alignment and produces fasta-like output: cat foo.maf | awk '/^s/{print ">" $2 "\n" $7}'.

[tim.ivanov.92]

Does it considerer blocks inside an alignment? cos thats the whole problem - different blocks may include different organisms