how to get gene string from NCBI genbank using Matlab 2010a
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I want to get gene string from NCBI genbank using Matlab . I have used getgebank() in matlab 2010a.but gettine error.
Data = getgenbank('NC_002695')
??? Error using ==> structfun
Inputs to STRUCTFUN must be scalar structures.
Error in ==> getncbidata>accession2gi at 343
queryDB = structfun(@(x)(str2double(x)),queryDB,'uniform',false);
Error in ==> getncbidata at 179 [giID,db] = accession2gi(accessnum,db,'quick');
Error in ==> getgenbank at 95
gb = getncbidata(accessnum,'fileformat','GenBank','database','nucleotide',varargin{:});
Will anyone please help me to resolve this?
Accepted Answer
Walter Roberson
on 23 Feb 2017
Edited: Walter Roberson
on 23 Feb 2017
I did not have R2010a handy but I tried in R2010b. I found that the XML returned by the query is
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>301 Moved Permanently</title>
</head><body>
<h1>Moved Permanently</h1>
<p>The document has moved <https://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi?term=NC_002695[Accession] here>.</p>
</body></html>
then it tries to find some information in that, gets an empty result, and then bombs trying to process the empty result.
The URL it is querying is http://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi?term=15829254[Accession] and if you put that into a browser that does get you somewhere useful, after redirection to https://eutils.ncbi.nlm.nih.gov/gquery?term=15829254%5BAccession%5D&retmode=xml . So it appears to be a matter of not handling the redirection.
Checking further, copying urls back and forth between versions, I notice that it is querying an http URL, and what works is querying the https url. When I try the https url on my OS-X system and running that old MATLAB R2010b version, I get a Java exception about it not being able to generate a DH pair, which is a problem in setting up HTTPS communications.
My testing shows that using https to connect works in R2013b but not R2012b; I am not going to bother to install R2013a just to test that version, since the end result is the same, that you need to upgrade because even if you hand-edited the relevant code to use https instead of http, your version of MATLAB would not be able to talk to the database.
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