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

[Daniel Lang]

Here is the answer from the EBI helpdesk.
Seems like we could loosen our restrictions for the ID line:)

I propose:
453c453
<               $temp_line = sprintf("%-11.10sstandard; $mol; $div; %d
BP.", $seq->id(), $len);
---
>               $temp_line = sprintf("%-10s standard; $mol; $div; %d
BP.", $seq->id(), $len);

Cheers,
Daniel

-------- Original Message --------
Subject: Re: EBI HELP: EMBL (Daniel.Lang at biologie.uni-freiburg.de) (rls)
(SUP#213519)
Date: Fri, 5 Nov 2004 01:52:17 GMT
From: support at ebi.ac.uk
To: Daniel.Lang at biologie.uni-freiburg.de

Hi,

The ID line description can be found in section 3.4.1 of the EMBL user
manual
which is at:

http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html

The items in that line are not bound by column positions at the moment.
Identifiers are not limited to 10 characters. Note that in the WGS data we
already have 12 character ID's. It has not been decided what the policy
will be
in future for cases where ID or basepair number become so large the ID
line will
exceed it present width. However, wrapping may be allowed as in the case
of AC
lines.

Hope this helps,

R:)

>Date: Thu, 4 Nov 2004 16:43:41 GMT
>From: w3nobody at ebi.ac.uk
>Reply-to: Daniel.Lang at biologie.uni-freiburg.de
>To: support at ebi.ac.uk
>Subject: EBI HELP: EMBL (Daniel.Lang at biologie.uni-freiburg.de)

> 
> EMAIL:        Daniel.Lang at biologie.uni-freiburg.de
> QUERY TYPE:   EBI HELP: EMBL (Daniel.Lang at biologie.uni-freiburg.de)
> REFERER URL:  http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
> IP:           132.230.186.106
> BROWSER:      Mozilla/5.0 (X11; U; Linux i686; rv:1.7.3) Gecko/20040913
> Firefox/0.10
> DATE:         Thursday 4 November 2004, 16:43
> 
> Hi,
> I´ve got a question concerning the ID line in an EMBL entry:
> Is there a length restriction for the entryname field in an EMBL entry?
> In the manual, I don\'t see any clear guidance about exact posisionings in the
> ID line.
> All the examples show the dataclass (usually  \"standard\") starting 11
> characters from the beginning of the entryname. 
> On the bioperl-list we are wondering how strict the standard is about the
length
> of the entryname and the positioning of the dataclass field.
> At the moment the Bioperl SeqIO::embl module keeps this distance, but limited
> the entryname to 10 chars to enforce a space between fields.  The
specification
> seems to include a space between entryname and dataclass, but that limits to
10
> char entrynames.
> 
> Thanks in advance,
> Daniel
> 
> 
> 
> 
> #########################################################################
-- 

Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

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