Python for generating BEAST2 XML files

[Terry Jones]

I just wrote some quick Python to generate BEAST2 XML files, either from the command line or for use in your own Python code.  See https://github.com/acorg/beast2-xml

It's currently very simplistic - there are many things that could be added. I'm not trying to replicate the whole of BEAUTi in Python, but am aiming to make it easy to programmatically (from the shell or from Python) generate BEAST2 config files without needing to use a GUI tool. The code currently has four simple templates to work from (based on clock model) if you don't provide one, all of which come straight from BEAUTi. It can make simple modifications to these. One workflow I imagine is that you set up a base template using BEAUTi, then you pass that to my code along with instructions for the modifications you want.

E.g., suppose you have a BEAST2 XML file (template.xml) you made with BEAUTi. You could write a (bash) shell loop like this:

$ for chainLength in 10000000 20000000 30000000

do

    for age in 10 20 30

    do

        for FASTA in file1 file2

        do

            beast2xml.py --templateFile template.xml --chainLength \
                $chainLength --age id1=$age --logFileBasename \
                ${chainLength}-${age}-${FASTA} \
                < $FASTA.fasta > config.xml

            beast-2 config.xml

            rm config.xml

        done

    done

done 

Or you can just use a default template, e.g., --clockModel relaxed-exponential.

There's more control if you're generating XML under Python mainly because you can use xml.etree.ElementTree (https://docs.python.org/3/library/xml.etree.elementtree.html) to manipulate the XML as much as you like.

Feedback welcome. I'd like to improve this (or, better, for you to improve it :-)), while hopefully keeping the code relatively simple.

Terry

[Andrew Rambaut]

Dear Terry,

I wrote a similar utility a while back (in Java). It is called ‘BEASTGen’ but actually can use templates for various phylogenetic input formats:

http://beast.community/beastgen

It might provide some ideas for this.

Best,

Andrew

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[Terry Jones]

Hi Andrew

Thanks for this - I just took a look.  I considered taking a route like that, but decided I didn't want to get the user to set up a config file to populate the template. That seemed like it was heading in the direction of just editing the XML directly (which after all is just a config file), and that I'd end up with an increasingly complicated config file (e.g., in JSON) that might come to resemble the XML in its complexity. I also took a very quick look at the BEAUTi code and saw the template files it has and its mechanism for indicating where things should be included. That might have been a better solution for me, but it also felt complicated (as someone who actually knows almost zero about the BEAST XML files). So I wrote something really simple, hoping that it wouldn't need to grow too much in complexity. The approach of letting the user make as complicated a base template as they want (using BEAUTi) and then making minor mods to it felt like a reasonable balance. It's a trade-off, of course, as you know :-)

Terry

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[Remco Bouckaert]

Hi Terry,

Thanks for your contribution. There have been other attempts to tackle the XML generating problem, all with a slightly different philosophy. This may be of interest:

http://www.beast2.org/2018/03/09/10-ways-to-generate-beast-xml.html

Cheers,

Remco

[Terry Jones]

Hi Remco

Thanks for adding the link :-)  It would be slightly more accurate to say it's "a Python class and command-line script to generate BEAST 2 XML files."  Also, there's a copy-paste error on the page: the BEASTShell also refers to BEAST2XML (though it links to the correct place).  Is there a link for Mixel?

Terry

[Remco Bouckaert]

Hi Terry,

Thanks for proofreading the post :-) I put in the fixes as you suggested.

I’ll check with Joseph, who wrote MiXeL whether the code is online somewhere.

Cheers,

Remco

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[Remco Bouckaert]

Hi Terry, 

MiXeL is now available via the blog post (http://www.beast2.org/2018/03/09/10-ways-to-generate-beast-xml.html) via this link: http://www.beast2.org/files/mixel.tar.bz2

Cheers,

Remco

[Terry Jones]

Hi Remco - great, thanks a lot for chasing that down. I'll take a look.

Terry

[Camila Duitama]

Hi!  

I am new to BEAST, and I will be conducting numerous experiments and replicates; therefore, I prefer not to use the GUI of BEAUti to produce the XML files. Is there a more standard method (since the last time this post was commented) to generate XML files for the latest version of BEAST (Beastv2.7.7) from the alignment files? I have tried Beast2XML (mentioned in this list: https://www.beast2.org/2018/03/09/10-ways-to-generate-beast-xml.html ) without success so far, as the format does not seem to be appropriate for the version of BEAST I am using.

Thanks,  

Camila

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