Based on the biopython help page here, I can filter the alignment columns based on first or last 10, I can even piece together subalignment using
align[:, :10] + align[:, -10:]
align being an MSA object, generated using
from Bio import AlignIO
align = AlignIO.read("Clustalw/opuntia.aln", "clustal")
But, is it possible to, say extract column based on list of position. For example, if i have a following list:
a=[12, 52, 68,45]
Is there a way to extract just these columns from the alignment align.
An R package called bio3d comes in handy to filter alignment by providing list as input (by doing: filtered_align = align[, a]), but would be great if i can use this from python.
Thank you
According to the Biopython docs, you can get column x with
align[:, x]
So the following should do the job for you:
from Bio import AlignIO
align = AlignIO.read("Clustalw/opuntia.aln", "clustal")
indices = [12, 52, 68, 45]
columns_as_strings = []
for column in indices:
columns_as_strings.append(align[:, column])