webread error 122 - after it has already worked

here is the relevent part of my code:

for i= (1:length(ralstonia_uncharacterized_idx));

if matrix_ralstonia(i)==1;

formatspec = 'https://www.UniProtKB.org/uniprot/%s.xml';

A1 = raw_ralstonia.ID{i};

url= sprintf(formatspec, A1);

o = weboptions('CertificateFilename','');

xml = webread(url,o);

%finding the general vicinity of name

expression = '<fullName evidence.*</fullName>';

gene_name_raw = regexp(xml, expression, 'match');

% focusing on the name

focused = '>.*<';

gene_name = regexp(gene_name_raw, focused, 'match');

raw_ralstonia.gene{i} = char(string(gene_name));

end

end

it has worked for many times, and now after a week I attended some other things I tried this again and it gives me the error massage:

Error using webread (line 122)

Could not access server. https://www.UniProtKB.org/uniprot/A0A0J9DKQ4.xml.

I didn't change a thing, and worked through the same terminal. I tried in other url's in another site, and the same error massage prompts.

WTH?

thanks in advance...

Answer 1

[Rashed Mohammed]

Hi Chaim

It seems like the domain name in the URL is not in use any longer. You can change the URL to https://uniprot.org/uniprot/A0A0J9DKQ4.xml and use the webread function.

Hope this helps !

[chaim giladi]

funny... now it worked, thank you!

but it happened too with a lot of other webreads and commands to the web, like in blast (blastncbi), even when I tried just copying code that worked for another guy. maybe I'll be able to come later with a better verse of my problem, after I deal further with blast.

[chaim giladi]

so now to the problem with blastncbi:

this one (just copied from a code that worked) doesn't work for me:

POI = 'MAEPQAESEPLLGGARGGGGDWPAGLTTYRSIQVGPGAAARWDLCIDQAVVFIEDAIQYRSINHRVDASSMWLYRRYYSNVCQRTLSFTIFLILFLAFIETPSSLTSTADVRYRAAPWEPPCGLTESVEVLCLLVFAADLSVKGYLFGWAHFQKNLWLLGYLVVLVVSLVDWTVSLSLVCHEPLRIRRLLRPFFLLQNSSMMKKTLKCIRWSLPEMASVGLLLAIHLCLFTMFGMLLFAGGKQDDGQDRERLTYFQNLPESLTSLLVLLTTANNPDVMIPAYSKNRAYAIFFIVFTVIGSLFLMNLLTAIIYSQFRGYLMKSLQTSLFRRRLGTRAAFEVLSSMVGEGGAFPQAVGVKPQNLLQVLQKVQLDSSHKQAMMEKVRSYGSVLLSAEEFQKLFNELDRSVVKEHPPRPEYQSPFLQSAQFLFGHYYFDYLGNLIALANLVSICVFLVLDADVLPAERDDFILGILNCVFIVYYLLEMLLKVFALGLRGYLSYPSNVFDGLLTVVLLVLEISTLAVYRLPHPGWRPEMVGLLSLWDMTRMLNMLIVFRFLRIIPSMKLMAVVASTVLGLVQNMRAFGGILVVVYYVFAIIGINLFRGVIVALPGNSSLAPANGSAPCGSFEQLEYWANNFDDFAAALVTLWNLMVVNNWQVFLDAYRRYSGPWSKIYFVLWWLVSSVIWVNLFLALILENFLHKWDPRSHLQPLAGTPEATYQMTVELLFRDILEEPGEDELTERLSQHPHLWLCR'
%Blast the inputted sequence against NCBI protein. Return 5000 results. 
[blastsend, waittime]=blastncbi(POI, 'blastp', 'MaxNumberSequences', 5000);

and the error massage is:

Error using webread (line 122)
Secure connection to
"https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Put&PROGRAM=blastp&COMPOSITION_BASED_STATISTICS=0&DATABASE=nr&FILTER=F&EXPECT=1.000000e%2B01&WORD_SIZE=3&MATRIX_NAME=BLOSUM62&GAPCOSTS=11+1&MAX_NUM_SEQ=5000&QUERY=MAEPQAESEPLLGGARGGGGDWPAGLTTYRSIQVGPGAAARWDLCIDQAVVFIEDAIQYRSINHRVDASSMWLYRRYYSNVCQRTLSFTIFLILFLAFIETPSSLTSTADVRYRAAPWEPPCGLTESVEVLCLLVFAADLSVKGYLFGWAHFQKNLWLLGYLVVLVVSLVDWTVSLSLVCHEPLRIRRLLRPFFLLQNSSMMKKTLKCIRWSLPEMASVGLLLAIHLCLFTMFGMLLFAGGKQDDGQDRERLTYFQNLPESLTSLLVLLTTANNPDVMIPAYSKNRAYAIFFIVFTVIGSLFLMNLLTAIIYSQFRGYLMKSLQTSLFRRRLGTRAAFEVLSSMVGEGGAFPQAVGVKPQNLLQVLQKVQLDSSHKQAMMEKVRSYGSVLLSAEEFQKLFNELDRSVVKEHPPRPEYQSPFLQSAQFLFGHYYFDYLGNLIALANLVSICVFLVLDADVLPAERDDFILGILNCVFIVYYLLEMLLKVFALGLRGYLSYPSNVFDGLLTVVLLVLEISTLAVYRLPHPGWRPEMVGLLSLWDMTRMLNMLIVFRFLRIIPSMKLMAVVASTVLGLVQNMRAFGGILVVVYYVFAIIGINLFRGVIVALPGNSSLAPANGSAPCGSFEQLEYWANNFDDFAAALVTLWNLMVVNNWQVFLDAYRRYSGPWSKIYFVLWWLVSSVIWVNLFLALILENFLHKWDPRSHLQPLAGTPEATYQMTVELLFRDILEEPGEDELTERLSQHPHLWLCR"
not established because "error setting certificate verify locations:
  CAfile: /etc/ssl/certs/ca-certificates.crt
  CApath: none". Check your system certificates for expired, missing, or invalid certificates.

Error in blastncbi (line 184)
    s = webread([site commandPut blastUrlString]);

so I see it uses webread, and I gather the problem is that here I can't add the part which exempts me from certification

o = weboptions('CertificateFilename','');
        xml = webread(url,o);
       

how could this be tackled?

thanks.