[Bioperl-l] Failed tests for FeatureIO
cjfields at uiuc.edu
Tue Sep 26 00:32:15 UTC 2006
On Sep 25, 2006, at 5:15 PM, Torsten Seemann wrote:
>> PS: is there any point to using mode() here? As Sendu points out,
>> no other Bioperl modules use it. Just curious...
> Many file formats that people use Bioperl to parse have this layout:
> LINE(S) FOR FEATURE 1
> LINE(S) FOR FEATURE 2
> Most of the modules (eg. Bio::Tools::*) don't parse HEADER until
> the first call of next_feature(), kind of like a pull parser.
> Unfortunately these same modules have methods to return data from
> the HEADER (eg. sequence_name), which return undef if you haven't
> read the first feature yet...
> My approach was to detect if the file handle was open for reading
> in _initialize(), so that I could parse the header before the first
> invocation of next_feature(), so that those HEADER-related methods
> would return the correct values no matter when called. It also
> makes the next_feature() implementation cleaner. The mode()
> detection is needed as the file/handle could actually be for
> write_feature() instead.
> If this is silly, I'll gladly accept advice for alternatives :-)
No, just curious. I hadn't seen mode() in use before.
> A related question: the header of a .ptt file has a line describing
> how many features are to follow after the header. How does this fit
> into the Bio::FeatureIO model? I guess I have to buffer up all the
> write_feature() calls, detect when the FeatureIO object is
> destroyed/out of scope, and then write the header and buffered
> features out?
> Any advice appreciated,
> Dr Torsten Seemann http://www.vicbioinformatics.com
> Victorian Bioinformatics Consortium, Monash University, Australia
I wrote an ERPIN parser a year ago that has a header followed by
data, similar to what you have above. I just ran a check on the first
iteration for the header, then flagged subsequent runs to bypass it.
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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