[Bioperl-l] Re: entrezgene binary ASN

Stefan Kirov skirov at utk.edu
Sat Oct 1 16:01:04 EDT 2005

As of now the parser does not seek through the streem, but hopefully it 
will as soon as I can sit down and do it (by the way it is weird but 
gene2xml will not parse the gunzipped file, so you should not use gzip -d).
I don't think you are missing anything as far as I can tell.

Hilmar Lapp wrote:

> I've tried to listen in on the exchange but I'm not sure I understand 
> what the issue is.
> I.e., does the parser need to seek in the stream? If yes, then piping 
> won't do any good if it works at all. If no, then the parser should be 
> perfectly fine with the filename being output from a pipe, and 
> possibly accept a file handle in substitution too. In that case, the 
> caller can pipe the actual input through any commands he/she wishes by 
> simply passing the piped command(s) (e.g. as in "gzip -d -c 
> file.asn.gz|gene2xml|").
> The parser doing this auto-magically isn't necessary and doesn't save 
> a caller that much. Instead, it exposes the parser to liabilities like 
> path of gzip, path of gene2xml and similar stuff which may not be 
> identical on all platforms.
> What am I missing?
>     -hilmar
> On Sep 30, 2005, at 12:55 PM, Michael Seewald wrote:
>> On 9/30/05, Mingyi Liu <mingyi.liu at gpc-biotech.com> wrote:
>>> I didn't say indexing would break, but the performance of retrieval
>>> would be horrible. That's why in most situations there's no need to use
>>> pipe - after all, any one who needs to use index & ID-based retrieval
>>> would convert the binary ASN to text file anyway (using a script,
>>> hopefully).
>> Absolutely right, seeking would be horrible.
>> Best wishes,
>> Michael
>> PS: And thanks for providing this great parser!!
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Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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