Bioperl-guts: bug attachments

Jeffrey Chang jchang@SMI.Stanford.EDU
Sun, 19 Mar 2000 22:16:54 -0800 (PST)


On Fri, 17 Mar 2000, Steve Chervitz wrote:

> Jeffrey Chang writes:
[Steve]
> Thanks for the pointer. I noticed that you have been saving the
> web-based reports as html whereas Cayte saved them as text. This has
> big consequences on the parsing strategy. Most importantly, the web
> based reports lack '>' characters at the start of each alignment
> section, which the bioperl blast parser depends on. It is best if web
> reports are saved as html, since one can pre-process them to generate
> a more standard-looking report with clever html stripping.

This makes sense.  We can't know which format users will choose to store,
and in this case, it's not too much harder to handle the complete format.

>  > Another thing that I've been thinking about, is that since the various
>  > bio* projects will benefit from good test sets, perhaps we should spin off
>  > another project to collect and manage them...
> 
> Good idea. Perhaps something like 'biodata' to house various flat file
> data formats and versions thereof.

Dang.  biodata is taken.  However, bioformats.org and biodataformats.org
are still available!

Jeff

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