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python posterior probability in stockholm file

I want to parse a multiple sequence alignment stockholm file by columns.

Is there any library or package in python to parse a multiple sequence alignment stockholm file and especially get the columns posterior probabilities??

P.s I went through AlignIo object from biopython, I couldn't find a way to get the posterior probability

python probability biopython msa alignment
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updated by Ram Ram • written by MAK • MAK

Can you post an example alignment file (here or using something like gist.github.com) which contains the per-column posterior probability numbers you want?

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written by Peter Peter

1 answer

These are present in the Stockholm file as per-colum annotation on each sequence, thus:

from Bio import AlignIO
align = AlignIO.read("alignment.sto", "stockholm")
for record in align:
    print(record.id)
    print(record.seq)
    print(record.letter_annotations["posterior_probability"])

Update: See https://github.com/biopython/biopython/issues/357 on not recording the per-column information in Stockholm files.

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written by Peter Peter

I need #GC pp_cons which is per column pp for all sequences and not #GR pp which is per residue pp for each sequence

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written by MAK • MAK

This will be supported in Biopython 1.66

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written by Peter Peter

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