XMFA to MAF

Question

[Lynda lyn]

Hi everyone :)

i want to convert my XMFA file (output of progressiveMauve) into MAF.

Has anyone had any luck converting xmfa into maf? And how did you do it?

Thanks :)

L

Answer 1

[Lynda lyn]

Thank you Seja Modha for your help :) i found this c++ script to convert xmfa to maf:

https://github.com/Wyss/mauve-py/blob/master/mauve/src/mauveAligner/src/xmfa2maf.cpp

[GenoMax]

Lynda Ait-Zai : I moved this to an answer since it does what you had originally asked for. You can accept this answer (use the green check mark) to provide closure for this thread.

[Raygozak]

There are no C++ scripts, only C++ programs.

Answer 2

[Sej Modha]

In past, I have used following script to convert xmfa to fasta. https://github.com/lskatz/lskScripts/blob/master/convertAlignment.pl

[Lynda lyn]

thank you Sej Modha :) i'll try it !

[Lynda lyn]

Hi Sej Modha , i tried the perl script. its works to have a fasta format but not to get the maf format.

Here is the output of my command:

$ ./transform_fasta.pl -i threeway.xmfa -o /home/lynda/Documents/threeway.maf -f maf

Converting threeway.xmfa (xmfa) to file /home/lynda/Documents/threeway.maf
------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::AlignIO::maf::write_aln" is not implemented by package Bio::AlignIO::maf.
This is not your fault - author of Bio::AlignIO::maf should be blamed!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.22.1/Bio/Root/Root.pm:447
STACK: Bio::Root::RootI::throw_not_implemented /usr/local/share/perl/5.22.1/Bio/Root/RootI.pm:741
STACK: Bio::AlignIO::maf::write_aln /usr/local/share/perl/5.22.1/Bio/AlignIO/maf.pm:189
STACK: main::convertAlnToFile ./transform_fasta.pl:99
STACK: main::convertAln ./transform_fasta.pl:41
STACK: main::main ./transform_fasta.pl:28
STACK: ./transform_fasta.pl:15
----------------------------------------------------------------

Thank you for the help !

[Sej Modha]

MFA stands for multiple fasta format so you should provide -f fasta parameter in the command.

[Lynda lyn]

When i add -f fasta, I get a maf file as output, but by opening the file It doesn't look like a maf file at all, it's a fasta format!. Maf contains more information than fasta format. Bio::AlignIO reads many formats but does not write in every format (the same is true for Bio::SeqIO). AlignIO currently supports output in these formats:

fasta
mase
selex
clustalw
msf
phylip
po
stockholm
XMFA
metafasta

[Sej Modha]

I am sorry but I have not written those scripts so I won't able to help much but you could try other built-in format available in Mauve and parse them to achieve what you are trying to do.

Supported alignment output formats are: phylip, clustal, msf, nexus, mega, codon