webread error 122 - after it has already worked

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chaim giladi
chaim giladi 2020-10-31
评论： chaim giladi 2020-11-3
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...

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回答（1 个）

Rashed Mohammed
Rashed Mohammed 2020-11-3
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 !
  2 个评论
chaim giladi
chaim giladi 2020-11-3
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
chaim giladi 2020-11-3
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.

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