[EMBOSS] Support for multi-line annotation in ig format

[Rozenbaum, Daniel (Biocceleration Inc)]

Hello Peter and everyone,

I was wondering if I could  revive the discussion about the support of IG format if possible. I'm helping deploy EMBOSS at the US Patent and Trademark Office, where this format, in its multi-line sequence annotation form, is used extensively.

Here's an example of an additional issue I've run into when trying to work with IG format in EMBOSS:

% makeprotseq -amount 10 -length 10 -nouseinsert -osformat ig -auto -osname ig1

% cat ig1.ig
;, 10 bases
EMBOSS_001
hcsptpstas1
;, 10 bases
EMBOSS_002
rdgwcvmtrm1
;, 10 bases
EMBOSS_003
fgtifgdgid1
<snip>

% entret  -sequence ig1.ig:EMBOSS_001 -nofirstonly -auto -stdout
;, 10 bases
EMBOSS_001
hcsptpstas1
;, 10 bases

In the entret result above the first annotation line of the subsequent record is returned as part of the requested record.

Many thanks,
Daniel
--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/ Office of Application Engineering & Development/ Patent System Division 
600 Dulany St.
Alexandria VA 22314

-------------------------
On 15/08/2012 17:57, Daniel Rozenbaum wrote:
> Dear list,
>
> (Peter, many thanks for your prompt reply to my previous inquiry!)
>
> We need to deal with extensive databases in Intelligenetics format with multiple lines in annotation of each record. It appears however that EMBOSS concatenates all annotation lines into a single line when building its internal representation of the sequence description:
>
> % cat /tmp/IGSEQ.ig
> ; Annotation line 1
> ; Annotation line 2
> ; Annotation line 3
> IGSEQ
> ACGCATCGCATCAGACTACGC1
>
>
> % seqret /tmp/IGSEQ.ig -osformat2 ig -auto -osname IGSEQ.emboss_ig2ig -osdirectory /tmp
>
>
> % cat /tmp/IGSEQ.emboss_ig2ig.ig
> ;Annotation line 1 Annotation line 2 Annotation line 3, 21 bases
> IGSEQ
> ACGCATCGCATCAGACTACGC1
>
> Are there any plans to support multi-line annotation in this format?

Interesting thought. We will take a look. It will need some care to 
maintain compatibility with other formats that have single (FASTA) or 
multiple (swissprot) descriptions.

Which package is using this IG format?

regards,

Peter Rice
EMBOSS Team