From iain.m.wallace at gmail.com  Mon Oct 10 07:57:13 2005
From: iain.m.wallace at gmail.com (Iain Wallace)
Date: Mon Oct 10 08:02:32 2005
Subject: [Bio-srs]
Message-ID: <8cff3eb80510100557g705a7ffco699fac8aad0ea0b6@mail.gmail.com>

Hi,

I am trying to return the embl entries for a list of uniprot entries.
I use the following command.
getz '(@testing > embl)'
where the file testing contains:
uniprot:CYGB_MOUSE
uniprot:GLB1_SCAIN

The output is:
EMBL:AK019410
EMBL:MMU315163
EMBL:BC055040

Is there any way of viewing the Uniprot ID's aswell as the EMBL ID;
My ideal output would be
EMBL:AK019410    UNIPROT:CYGB_MOUSE
EMBL:MMU315163 UNIPROT:CYGB_MOUSE
EMBL:BC055040     UNIPROT:CYGB_MOUSE

I have tried getz '(@testing > embl) > uniprot'
but this only returns one entry, rather than three..

I want to parse out the results into individual files according to the
uniprot id.

I believe it is possible using views and wgetz, but I would prefer not
to use wgetz

Any help would be greatly appreciated.

Iain

From iain.m.wallace at gmail.com  Mon Oct 10 07:57:15 2005
From: iain.m.wallace at gmail.com (Iain Wallace)
Date: Mon Oct 10 08:03:11 2005
Subject: [Bio-srs] Uniprot and EMBL question
Message-ID: <8cff3eb80510100557x58552b5u4c4b80939fb7d02a@mail.gmail.com>

Hi,

I am trying to return the embl entries for a list of uniprot entries.
I use the following command.
getz '(@testing > embl)'
where the file testing contains:
uniprot:CYGB_MOUSE
uniprot:GLB1_SCAIN

The output is:
EMBL:AK019410
EMBL:MMU315163
EMBL:BC055040

Is there any way of viewing the Uniprot ID's aswell as the EMBL ID;
My ideal output would be
EMBL:AK019410    UNIPROT:CYGB_MOUSE
EMBL:MMU315163 UNIPROT:CYGB_MOUSE
EMBL:BC055040     UNIPROT:CYGB_MOUSE

I have tried getz '(@testing > embl) > uniprot'
but this only returns one entry, rather than three..

I want to parse out the results into individual files according to the
uniprot id.

I believe it is possible using views and wgetz, but I would prefer not
to use wgetz

Any help would be greatly appreciated.

Iain

From hpm at ebi.ac.uk  Mon Oct 10 09:38:59 2005
From: hpm at ebi.ac.uk (Hamish McWilliam)
Date: Mon Oct 10 19:57:31 2005
Subject: [Bio-srs] Uniprot and EMBL question
In-Reply-To: <mailman.32.1128949390.18885.bio-srs@net.bio.net>
References: <mailman.32.1128949390.18885.bio-srs@net.bio.net>
Message-ID: <434A7D03.2050402@ebi.ac.uk>

Hi Iain,

> I am trying to return the embl entries for a list of uniprot entries.
> I use the following command.
> getz '(@testing > embl)'
> where the file testing contains:
> uniprot:CYGB_MOUSE
> uniprot:GLB1_SCAIN
> 
> The output is:
> EMBL:AK019410
> EMBL:MMU315163
> EMBL:BC055040
> 
> Is there any way of viewing the Uniprot ID's aswell as the EMBL ID;
> My ideal output would be
> EMBL:AK019410    UNIPROT:CYGB_MOUSE
> EMBL:MMU315163 UNIPROT:CYGB_MOUSE
> EMBL:BC055040     UNIPROT:CYGB_MOUSE
> 
> I have tried getz '(@testing > embl) > uniprot'
> but this only returns one entry, rather than three..
> 
> I want to parse out the results into individual files according to the
> uniprot id.
> 
> I believe it is possible using views and wgetz, but I would prefer not
> to use wgetz

A simple solution is to use a shell script to do the relevant 
processing. For example:

   #!/bin/sh
   tab=`echo "\t"`
   for ln in `cat testing`;  do
     getz "[$ln]>embl" | sed "s#\$#$tab$ln#"
   done

This produces your desired result, but is inefficent for large lists of 
ids since each id is processed using an individual getz call.

If your set of ids is the product of a query you could use an Icarus 
script to do the processing instead, and avoid some of the overhead 
involved in the getz calls.

Hamish
-- 
============================================================
Mr Hamish McWilliam
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD, UK

URL: http://www.ebi.ac.uk/
============================================================