[Bioperl-l] Re: entrezgene binary ASN

Hilmar Lapp hlapp at gmx.net
Sat Oct 1 15:48:26 EDT 2005

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 

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?


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!!
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

More information about the Bioperl-l mailing list