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Gmane
From: Adam =?iso-8859-1?Q?Sj=F8gren?= <asjo <at> koldfront.dk>
Subject: Re: Question about retrieving sequences from swissprot database
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 29th July 2013 18:54:15 UTC (over 3 years ago)
cacaucenturion2  writes:

> I met a problem when trying to retrieve sequences from SWISSPROT. I
> tried the following script

> perl -e 'use Bio::Perl; $seq_object =
get_sequence('swissprot',"Q197F7");' 

> However I was told that 

> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: acc Q197F7 does not exist

Your one-liner works for me:

  $ perl -E 'use Bio::Perl; $seq_object =
get_sequence('swissprot',"Q197F7"); say $seq_object->seq' 
 
MYQAINPCPQSWYGSPQLEREIVCKMSGAPHYPNYYPVHPNALGGAWFDTSLNARSLTTTPSLTTCTPPSLAACTPPTSLGMVDSPPHINPPRRIGTLCFDFGSAKSPQRCECVASDRPSTTSNTAPDTYRLLITNSKTRKNNYGTCRLEPLTYGI
  $ 

Maybe you are behind a firewall, or somehow blocked?


  Best regards,

    Adam

-- 
 "den der noget klæge symfoniske letmetal-blanding af         Adam
Sjøgren
  Beatles, Zeppelin, Kansas og Thin Lizzy var sgu ikke   [email protected]
  lige min kop te"
 
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