[Bioperl-l] Length of ID in EMBL sequence entries

simon andrews (BI) simon.andrews at bbsrc.ac.uk
Fri Nov 5 05:49:52 EST 2004

> -----Original Message-----
> From: Daniel Lang [mailto:daniel.lang at biologie.uni-freiburg.de] 
> Sent: 05 November 2004 08:41
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Length of ID in EMBL sequence entries
> Here is the answer from the EBI helpdesk.
> Seems like we could loosen our restrictions for the ID line:)
> I propose:
> < sprintf("%-11.10sstandard;
> > sprintf("%-10s standard;

Err, don't those two equate to the same thing?

If we're allowing 12 char IDs then that would be:

$temp_line = sprintf("%-13.12sstandard; $mol; $div; %d
BP.", $seq->id(), $len);

But if we take what the EMBL said literally then we don't actually need
to restrict the id length at all:

$temp_line = sprintf("%s standard; $mol; $div; %d
BP.", $seq->id(), $len);

..but that would seem to be asking for trouble if someone were to pass
it a really large ID.  I suppose the pragmatic limit would be to not
allow the ID to be long enough to make the ID line longer than 80 chars,
but that would require some extra logic due to the variation in length
of the sequence length, and would impose a non-standard ID length limit.



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