webread error(ncbi)

im trying to get some information from ncbi website using this code:

HepatitisC = getgenbank('NC_004102');

HepatitisC = HepatitisC.Sequence;

Hepatitisc_length = length(HepatitisC);

first_300_bases = seqdisp(HepatitisC(1:300));

figure

ntdensity(HepatitisC)

bases = basecount(HepatitisC);

figure

basecount(HepatitisC,'chart','pie');

title('Distribution of Nucleotide Bases for Hepatitis C Virus');

figure

dimers = dimercount(HepatitisC,'chart','bar');

title('Hepatitis C Dimer Histogram');

seqshoworfs(HepatitisC);

orfs = seqshoworfs(HepatitisC,'AlternativeStartCodons',true);

AND I RECIVE THIS ERROR:

Error using webread (line 122)

The connection to URL

'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=NC_004102%5BAccession%5D' timed out after 5

seconds. Set options.Timeout to a higher value.

Error in getncbidata>accession2gi (line 315)

searchXML = webread(searchurl);

Error in getncbidata (line 181)

[giID,db] = accession2gi(accessnum,db,'quick');

Error in getgenbank (line 76)

[varargout{1:nargout}] = getncbidata(accessnum,'fileformat','GenBank','database','nucleotide',varargin{:});

Error in Hepatitis (line 1)

HepatitisC = getgenbank('NC_004102');

im new to matlab and i dont know how to solve this.

thanks

Answer 1

[Rahul]

Hi @arash manbu,

I understand that you face the mentioned error of 'webread' while trying to obtain the data using 'getgenbank'. You can consider the following options to read the data correctlty:

• Set a higher timout using the 'weboptions' function.
• Obtain the data in a txt file using the 'websave' function with the weboptions defined.
• Now read the data from the txt file using 'getbankread' function.

Here is an example:

wo = weboptions("Timeout", 10);
websave("output.txt", "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=950361812&rettype=gb&retmode=text&seq_start=6022&seq_stop=17213", wo);
data = genbankread("output.txt");

In recent MATLAB versions this issue has been resolved and just accessing data using 'getgenbank('NC_004102')' does not give the error.

The following MathWorks documentations can be referred:

'getgenbank': https://www.mathworks.com/help/bioinfo/ref/getgenbank.html

Thanks.