Does Biopython Have Something Like Perl'S Bio::Locatableseq To Map Positions To Columns And Back Again

Question

[Owen S.]

Hi,

In the past I have happily used perl's Bio::LocatableSeq to map positions in one sequence to positions in another. Does biopython's Bio.Align not have similar functionality?

Here is what I want. Given the following Align object:

from Bio.Alphabet import generic_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
a = SeqRecord(Seq("AAAACGT", generic_dna), id="Alpha")
b = SeqRecord(Seq("AAA-CGT", generic_dna), id="Beta")
c = SeqRecord(Seq("AAAAGGT", generic_dna), id="Gamma")
align = MultipleSeqAlignment([a, b, c])

I want to be able to do this kind of thing:

align.position_to_column(seq=1, pos=2)
2

align.position_to_column(seq=1, pos=3)
4

align.column_to_position(seq=0, col=3)
3

align.column_to_position(seq=1, col=3)
None

I find it hard to believe this isn't part of Align, but I haven't been able to find any examples of this in python. Thanks in advance.

Answer 1

[Peter]

Does this do what you want? http://biopython.org/wiki/Coordinate_mapping

Feedback on the mailing list please :)

[Owen S.]

Thanks Peter. I didn't know about Coordinating_mapping, but it's not quite what I was looking for. This looks to me like a way of mapping genomic, mRNA, and protein coordinates (using a GenBank "or similar file" as input). I was looking for something that maps positions between sequences in an alignment (using an alignment file as input).

By the way, in pythonland, what exactly do we call a collection of code like Coordinate_mapping? It doesn't seem to be part of BioPython. It's just somebody's branch in their personal, public git repos, with a description on the biopython wiki? Are there hundreds of such branches? If so, it seems to me that BioPython would benefit from a package management system like R has (CRAN or bioconductor). Or am I missing something?

Actually, I guess I see from https://github.com/biopython/biopython/network that this is more of a special situation, where we have some code being worked on by a developer, which will (may) be merged back into the main codebase in the future.

[Peter]

That wiki page is pointing at an experimental branch on GitHub - if we had some positive feedback that this is widely useful, then it would probably end up in Biopython proper.

See also http://www.slideshare.net/pjacock/biopython-update-bosc2013/ for some thoughts on Biopython packaging and PyPI, https://pypi.python.org/pypi