[EMBOSS] getting organism from accession

[Tiwari, Bela]

Thanks Richard. The script looks handy and at minimum may help me deal with searching for my identifiers in more than one database.

cheers,

Bela


*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental
Bioinformatics Centre
http://nebc.nerc.ac.uk
tel: 01491 69 2705

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
*************************
________________________________________
From: Richard Rothery [rrothery at ualberta.ca]
Sent: 18 June 2010 15:54
To: Tiwari, Bela
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] getting organism from accession

I have a perl script written by Craig Knox of the University of Alberta
Bioinformatics help desk that does this. I have attached it FYI. It is
slow, but gets the job done.

Output can be fed to gnumeric etc.

Richard




On Fri, 2010-06-18 at 13:07 +0100, Tiwari, Bela wrote:
> Dear all,
>
> I have a set of accession numbers and I want to retrieve the organism that the sequence is associated with - i.e. the content of the OS line in an embl file.  I don't need the taxonomic id, and I don't need to start traversing taxonomy trees. I want to do this by accessing remote databases (via srs, as configured in my emboss.defaults file), rather than indexing databases locally.  So the output I want would be a text mapping like:
>
> accession : species
>
> where species is taken from the OS line of a database entry.
>
> The closest I've made it to using Emboss is to get the gff output file containing feature information using a command along the lines of:
>
> seqret -feature embl:XXXX -oufo2 myfeat.txt
>
> (embl is a database I can search using srs as configured in my emboss.defaults file.) The first non-hashed line in the file myfeat.txt contains the term
>
> "organism="Whateverus thingus"
>
> so I could parse that out. However, this file still contains a lot of extra (unwanted) information and requires parsing.
>
> Does anyone know if I'm missing something obvious in Emboss that I could use for this?
>
> (I have tried the BioPerl route to get this info from the NCBI, and apart from being unwieldly, I'm managing to get the wrong organism returned for the type of identifer I have. No, I haven't spent time tracking down the problem - frankly, I'd rather resove it using Emboss and/or srs calls.)
>
> If there isn't anything that will do the job in Emboss at the moment, is there any chance I can put in a development request for an extra flag for seqret, or an extra utility tool that might accomplish this task?
>
> cheers,
>
> Bela
>
> *************************
> Dr. Bela Tiwari
> Lead Bioinformatician
> NERC Environmental
> Bioinformatics Centre
> http://nebc.nerc.ac.uk
> tel: 01491 69 2705
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
> *************************


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