Reading character matrices into memory one by one

[Markus Englund]

Hi,

Is there some way to read and process multiple character matrices in a file one by one so I don't have to load them all into memory at the same time?

The pseudocode might look something like this:

Open the input file for reading

Read character matrix 1 into memory

Process character matrix 1

Read character matrix 2 into memory

Process character matrix 2

…

Close the input file

Cheers,

Markus

[Jeet Sukumaran]

This would definitely be useful and can be implemented. However this
would have to be done at the parser level, and thus each file format
would need to have a different implementation. I presume you mean for
NEXUS or NeXML format, as neither Phylip nor FASTA standards specify
multiple alignments in their standard?

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[Markus Englund]

Sounds great! I was primarily thinking of the NEXUS format in my case. I suppose it could also be implemented for the Phylip format, even if the standard does not specify multiple matrices. I know that for example PhyML do read multiple alignments in that format.

Best,

Markus

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[Jeet Sukumaran]

I think it would be valid to support this feature in NEXUS. I would not
be so enthusiastic about Phylip because it mean introducing an arbitrary
non-standard convention to describe the multiple matrices.

So, the good news is "yes, we can". The bad news is that I cannot
promise when it will happen! If you don't mind submitting an issue on
the github page, I can promise that it will make the "todo" list,
though. Which is the best I can promise right now :)

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[Markus Englund]

NEXUS format will be just fine! I understand that time is limited. I'll create a feature request on GitHub.

Markus

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