[Biopython-dev] Bioformat module

Andrew Dalke adalke at mindspring.com
Sun Dec 30 08:37:12 EST 2001

Hey all,

  Here's the first go at a module based off the set of emails
I wrote last week.  It's at

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.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.

                    dalke at dalkescientific.com

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