[BioPython] Sequence from Fasta

[Leighton Pritchard]

Hi,

Just to chip in my two-pennorth, there's a self-defining tab-separated
format called "Axon Text File Format" that might be useful here, and which
is frequently seen in microarray work.  There's a description of its use for
.gal files here:

http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html

It's fairly flexible and straightforward as a format, and allows for
human-readable headers - which can contain column definitions, content
notes, or anything else you like - that is adaptable to a variety of output
conventions.  Of course, getting people to settle on a convention is the
tricky part, but at least any given file might be well-defined in its
headers while people argue over it ;)

It's hardly likely that going down that route in BioPython will result in an
file convention that's accepted industry-wide, but at least it might give
options for writing out FASTA file content in tab-separated form while
unambiguously retaining ID, name and definition strings along with the
sequence. 

L.

On 01/07/2008 17:06, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

> Giovanni wrote:
>> yes, I think it will be useful to implement.
>> I know of people who have written a customized fasta2tab script and
>> use it quite frequently, so it would be good to support such a task.
>> As you said before this format is commonly used in combination with
>> grep/gawk scripts.
> 
> I've gone for the simple option about how to parse the first field, its used
> as the record identifer (.id) and name only (nothing clever).  Here is my
> suggested code, which you are welcome to download and try out.
> 
> Bug 2533 - Support for simple "tab" format in Bio.SeqIO
> http://bugzilla.open-bio.org/show_bug.cgi?id=2533
> 
> If you want to try this yourself you'll need to download the new file
> TabIO.py into the Bio/SeqIO folder and update Bio/SeqIO/__init__.py to
> tell it about the new format (two new lines, see patch).
> 
> Peter
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-- 
Dr Leighton Pritchard B.Sc.(Hons) MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
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