Option 1 that I used:
1. Convert xmfa to fasta using the script convertAlignment.pl (found online
https://github.com/lskatz/lskScripts/blob/master/convertAlignment.pl)
perl ./convertAlignment.pl -i inputfilename.xmfa -o
outputfilename_step1_int.fasta -f fasta -g xmfa -c
2. Convert the output from step 1 into a sequential fasta file with this
command:
perl -MBio::SeqIO -e 'my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format =>
'fasta'); while (my $seq = $seqin->next_seq) { print
">",$seq->id,"\n",$seq->seq,"\n"; }' < ouputfilename_step1_int.fasta >
outputfilename_step2_seq.fasta
3. Remove all the weird little characters that get added to the sequence names
by the script (hashtags etc)
Option 2, which, if I recall correctly, doesn't require any additional steps:
Use this script:
https://github.com/kjolley/seq_scripts/blob/master/xmfa2fasta.pl
perl xmfa2fasta.pl --file inputfile.xmfa > outputfile.fasta
From: TATIANA MURILLO CORRALES
<tatiana.murillocorra...@ucr.ac.cr<mailto:tatiana.murillocorra...@ucr.ac.cr>>
Date: Sunday, June 12, 2016 at 10:37 PM
To:
"Mauve-users@lists.sourceforge.net<mailto:Mauve-users@lists.sourceforge.net>"
<Mauve-users@lists.sourceforge.net<mailto:Mauve-users@lists.sourceforge.net>>
Subject: [Mauve-users] Whole genome alignment for Gubbins
Hello dr. Darling and Mauve users,
I am interested to generate whole genome alignments with Mauve in order to
analyse them with Gubbins. I wanted to ask for advice on how would be the best
way to transform the xmfa files produced with Mauve to multifasta as in input
for Gubbins.
Thank you,
Tatiana Murillo
--
Tatiana Murillo Corrales
Research Centre for Tropical Diseases
University of Costa Rica
San José, Costa Rica
Phone number +50625118616
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