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
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tim.ivanov.92 •
Does it considerer blocks inside an alignment? cos thats the whole problem - different blocks may include different organisms
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MAF to Fasta or XMFA - how does it work?
Need A Unix Script For The Galaxy Tool: Maf To Fasta (Version 1.0.1)
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