[emboss-dev] Specifying sequence lists for seqret
naktinis at csc.fi
Thu Jul 29 13:28:57 UTC 2010
On 07/29/2010 03:28 PM, Peter Rice wrote:
> On 29/07/10 12:47, Rimvydas Naktinis wrote:
>> I'm developing EMBOSS integration into Chipster project
>> (chipster.csc.fi). I was wondering if there's a way to specify sequence
>> list (for example, when calling seqret) without creating any extra files?
>> I know there's a way to do it like this:
>>> seqret @sequencelist
>>> seqret list:sequencelist
>> But what I would need would look something like:
>>> seqret "swiss:CASA1_RABIT,swiss:CASA1_HUMAN"
>> I've looked into USA format specification and it seems that there is
>> actually no way to do it without creating some temporary file. Or am I
>> missing something?
> We can add that as an option ... but there is a very real danger that
> the command line will be too long.
> How many sequences will be on the command line (normal use, and worst case)?
> Peter Rice
In current use case user enters the sequence names manually, so list
should not be very long.
However, we should also think about a general case. As far as I know,
starting from Linux kernel version 2.6.23 argv size is limited by 1/4th
of memory stack size
so argument length is basically limited only by available physical
memory. Situation might be different with other operating systems. I
guess in Windows the limit is 32Kb
I guess this could be left for programmers to deal with and users, who
use the command line themselves, would probably use the @seqlist option
for long lists anyway.
And thanks for quick response!
CSC — IT Center for Science Ltd
More information about the emboss-dev