Hi Aaron,
Many thanks for your reply, it was really helpful. I created a batch file
and run that command for each of the alignments. It worked perfectly for
most of them but got the same error for the rest, for instance:
Loading alignment file...106 LCBs before splitting with
getSplitLCBs(XmfaViewerModel).
starting with 21 LCBs
genome0 21
genome1 21
genome2 21
genome3 21
genome4 21
genome5 21
genome6 21
genome7 21
genome8 21
genome9 21
genome10 21
genome11 21
genome12 21
21 LCBs after splitting with getSplitLCBs(XmfaViewerModel).
Exporting SNPs...
java.lang.ArrayIndexOutOfBoundsException: genome genome.fas position 2433327
at org.gel.mauve.XMFAAlignment.getLCB(Unknown Source)
at org.gel.mauve.XmfaViewerModel.getLCBIndex(Unknown Source)
at org.gel.mauve.analysis.SnpExporter.getSNPs(Unknown Source)
at org.gel.mauve.analysis.SnpExporter.getSNPs(Unknown Source)
at org.gel.mauve.analysis.SnpExporter.export(Unknown Source)
at org.gel.mauve.analysis.SnpExporter.main(Unknown Source)
I guess it is some bug in accessing memory, although happened with both
alignments from 3 to more than 60 genomes, and the genome sizes are not
that different.
Thanks for your help
Leonor Sanchez
2014/1/23 Aaron Darling <aaron.darl...@uts.edu.au>
> Hi Leonor,
>
> Yes, it is possible to export a list of SNPs from the command-line if
> you are using one of the snapshot releases available from here:
> http://gel.ahabs.wisc.edu/mauve/snapshots
>
> The command-line syntax to do so is:
>
> java -cp Mauve.jar org.gel.mauve.analysis.SnpExporter -f aln.xmfa -o
> aln.snps
>
> Hope that helps,
> -Aaron
>
>
>
> On Wed, 2014-01-22 at 06:53 +1100, Leonor Sanchez wrote:
> >
> > Hi,
> >
> >
> > I was wondering if there was any way of using the module for
> > extracting the SNP list using the command line. I am working with
> > hundreds of alignments and I would find that very useful. I've read in
> > the list that other people were also asking for that some time ago but
> > I cannot find the answer. As the manual says, contigs can be reordered
> > using the terminal, is there also a instruction for the SNP list
> > extraction?
> >
> >
> > Thanks in advance!
> >
> >
> >
> > Leonor Sánchez
> >
> >
> >
> >
> > --
> > Leonor Sánchez Busó
> > PhD student
> > CSISP - Centro Superior de Investigación en Salud Pública / Centre for
> > Public Health Research
> > Área de Genómica y Salud / Genomics and Health
> > Av. de Catalunya, 21
> > 46020 Valencia, Spain
> > Tel: +34 - 961925967 (Ext. 925967)
> > sanchez_leo...@gva.es
> >
> >
> >
> >
> >
> >
> > --
> > Leonor Sánchez Busó
> > PhD student
> > CSISP - Centro Superior de Investigación en Salud Pública / Centre for
> > Public Health Research
> > Área de Genómica y Salud / Genomics and Health
> > Av. de Catalunya, 21
> > 46020 Valencia, Spain
> > Tel: +34 - 961925967 (Ext. 925967)
> > sanchez_leo...@gva.es
> >
> >
>
> --
> Aaron E. Darling, Ph.D.
> Associate Professor, ithree institute
> University of Technology Sydney
> Australia
>
> http://darlinglab.org
> twitter: @koadman
>
>
>
> UTS CRICOS Provider Code: 00099F
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--
*Leonor Sánchez Busó*
PhD student
CSISP - Centro Superior de Investigación en Salud Pública / Centre for
Public Health Research
Área de Genómica y Salud / Genomics and Health
Av. de Catalunya, 21
46020 Valencia, Spain
Tel: +34 - 961925967 (Ext. 925967)
sanchez_leo...@gva.es
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