[Biopython-dev] Status of SearchIO

[Eric Talevich]

On Fri, Oct 26, 2012 at 8:54 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
> If the namespace nesting bothers you, then you might not like
> my thoughts for how to combine Bio.Align and Bio.AlignIO
> (since we can't use Bio.align due to the folder name clash on
> case incentive platforms): I was wondering about using
> Bio.seq.align for this, which again is a bit nested but would
> make it a system module to Bio.seq.search (aka SearchIO)
> and Bio.seq.record (which could include the former SeqIO
> code as well as the SeqRecord class).
>
>
Does that mean we'd have read, write, convert, etc. under Bio.seq.record?
This is how that API would look:

from Bio.seq import record
for rec in record.parse("example.fa", "fasta"): ...

As opposed to:

# Minor change
from Bio import seqio
for record in seqio.parse(...)

# Make sure we get those relative imports right!
from Bio.seq import io
for record in io.parse(...)

# Slight cognitive distance, but maybe worth it
from Bio import seq
for record in seq.parse(...)


Also: Technically, Bio.Motif operates on multiple sequence alignments, so
it could be moved to Bio.seq.align.motif. (Not entirely trolling here, just
pointing out possible consequences.)

-Eric