online extracting data from DB using MATLAB

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Neeloufar 2015-4-15

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关闭： MATLAB Answer Bot 2021-8-20

Hello I want to extract DNA sequence (NT seq) from http://www.genome.jp/dbget-bin/www_bget?eco:b0002 web site with matlab. I do not know what to do. I have to do this only by matlab, so I have no other chance to work with other languages. I was wondering if anyone helps me to solve this problem. by the way I have use some function getTableFromWeb_mod which is written in matlab, but when I used this function I faced with 3 warnings and nothing return. It would be grateful if someone help me, and also when I run the code bellow I confront with that warnings again, the same.

FirstfullURL = ('http://www.genome.jp/dbget-bin/www_bget?eco:b0002/search/apachesolr_search/<NP seq> '); Firststring = urlread(FirstfullURL);

Thanks

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Answer 1

Jonathan Campelli 2015-4-15

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Hello Neeloufar,

Here is some very specific code that pulls all the data from url: GenomeNet NT seq:

pullData=urlread('http://www.genome.jp/dbget-bin/www_bget?-f+-n+n+eco:b0002')
% pullData(pullData == ' ') = []
Cut=strsplit(pullData, {'(N)','</pre>'})
char(Cut(2))

The DNA sequence is targeted by cutting the downloaded string into three segments, the middle of which is found at "Cut(2)" and returns a readable string using "char(Cut(2))". Let me know if this code does not meet your needs.

Best regards,

Jonathan Campelli