[Biopython-dev] Bioformat module

[Andrew Dalke]

Hey all,

  Here's the first go at a module based off the set of emails
I wrote last week.  It's at
  http://www.biopython.org/~dalke/Bioformat-0.1.tar.gz

No setup.py or anything fancy like that.  Though you do
need the lastest version of CVS Martel.  (List of changes
in the next email.)

In theory this provides a platform for:
  - automatic format recognition
  - using the format information to build a data structure
  - writing that data structure to another format

For example, these parts can be put together for simple,
generic file conversion, as in:

from Bio import SeqRecord

writer = SeqRecord.io.make_writer(sys.stdout, "fasta")
writer.writeHeader()  # needed for some formats
for record in SeqRecord.io.read(open("file.unknown")):
  writer.write(record)
writer.writeFooter()  # needed for some formats

(Actually, with the code as-is, this is done with

from Bioformat import IO
IO.io.convert(infile = open("file.unknown"), output_format = "fasta")

:)

The README includes some examples of how to use this module.
Please take a look.

More after I have a chance to get some sleep.  This project
was harder than I thought it would be.  OTOH, it's something
that should be very exciting for the O'Reilly conference.

                    Andrew
                    dalke at dalkescientific.com