Bioperl-guts: Heads up for 0.05
Mon, 8 Mar 1999 09:05:22 +0000
On Sun, 7 Mar 1999, Aaron J Mackey wrote:
> I'll take care of writing tests for the DB stuff, in which I'll check for
> the ability to open a socket (i.e. use the internet). I believe that the
> DB implementations currently throw if they can't get a socket to use, but
> I'll double check and make sure.
That is something to check.
Ideally, if there is not internet connection, the test script should
print out "Can't test DB/GenBank and DB/GenPept" because of no internet
connection, *but still pass the test*.
>From experience, I know that even if you say "test 12 will fail if no
internet connection" people will get frantic if any test fails, even if
they are told to expect it
> I'll also write a SeqIO::Genbank and SeqIO::ASN1.1, but with Seq.pm that's
> not much. What's the status with SeqFeature/Entry/WhateverItsCalledNow,
> is someone working on it? I think having SeqIO streams for fancy formats
> would be great, but only if we can actually get at the information
> contained within. (Note:: currently DB::GenBank/Pept is only getting the
> fasta-formatted data from ncbi, and populating a Seq.pm object - this is
> an area where a SeqIO::Genbank -> Entry.pm object would be useful).
I am working on it. Well - designing it - (take a look at
Projects/SeqAnnot on the web page). This still needs quite alot of
thought, although Steve and I reckon that we have quite a good angle on
the overall design
It will not be in 0.05 sadly. I hope it will be in by 0.06. But I agree
it is a real necessity. Aaron - if you want to list your requirements
for the object that would be great. I *don't* think that we should
necessarily just have everything that is in ncbi/embl databases, but that
is a starting point. Functional requirements (I want to be able to do xxx
to the object) is also really helpful.
> On another note, we need to make sure that people don't use DB::Genbank to
> send multiple successive requests to ncbi (or any other web server), but
> rather to use batch-query mode (not currently implemented, but I'm working
> on it). I got spanked earlier this week for stupidly slamming the ncbi
> server with >2000 hits/hour. Mea culpa, mea culpa ...
I don't know how we stop this. (do you mean, having a counter for each
request in a session issued, and start throwing warnings after 100
> As far as interfacing DB-retrieved Seq's with Index'ed databases, I'd
> suggest to leave it to the user:
The indexing doesn't work this way. It is more about whether this call
> (I haven't actually looked at the Index stuff yet, so forgive me if my
> syntax is inaccurate, but you get the idea).
> DB is a one way street (stream?) -> ask for Seq, get Seq. What you want
> to do with it is up to the user (crunch it, fragment it, index it, etc).
> o ~ ~ ~ ~ ~ ~ o
> / Aaron J Mackey \
> \ Dr. Pearson Laboratory /
> \ University of Virginia \
> / (804) 924-2821 \
> \ firstname.lastname@example.org /
> o ~ ~ ~ ~ ~ ~ o
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