Hi, probably the wrong place to discuss such things, but your file looks like you forgot to reappend the newline characters after you read your line. When you write out the line, append a "\n". This results in a file similar to this:
stringId ncbiTaxonId taxonName preferredName annotation 9606.ENSP00000333813 9606 Homo sapiens ALG12 Dolichyl-P-Man:Man(7)... ... So String-DB seems to report in some tab delimited format. I don't know String-DB and can only guess what sort of information is provided, but for me, this simply maps the String-ID to an NCBI Taxons (and its preferred name) and reports the prefered name (ALG12 in this example) of the mapped protien and its String-DB annotation. cheers, -thasso On Dec 18, 2009, at 22:00 , jitesh dundas wrote: > Dear Dr. Thasso Griebel , > > Finally I have got the output! It was a simple mistake from my side. > > The program needed was for just to read from the URL and not POST to > the URL. > > I have attached the working code now. > > Now the problem is that I dont understand what that means. How to I > understand what part is the list of protein interactors for the > given term. > > Can some one help me in this ? All this is new to me. > > Regards, > Jitesh > > On Fri, Dec 18, 2009 at 11:47 PM, Thasso Griebel > <[email protected] > > wrote: > Hi, > > uh yeah...bioinformatics...sort of :) > > In general I think you have to be a bit more precise about the error > you get and you might want to append a stacktrace or something. > "Version number" error sounds like a "class version number" ? But I > have no idea, could be anything. > > I can confirm though that the data URL is fine > http://string-db.org/api/tsv/resolve?identifier=ADD&species=9606 > . Here is the method I used to fetch the data: > > public static void write2File(URL url, File file) throws IOException { > FileOutputStream out = null; > InputStream in = null; > try { > in = url.openStream(); > out = new FileOutputStream(file); > byte[] buff = new byte[4096]; > int len = 0; > while (-1 != (len = in.read(buff))) { > out.write(buff, 0, len); > } > } finally{ > if(out != null)out.close(); > if(in != null) in.close(); > } > } > > > with this and your URL a simple > > write2File(new > URL("http://string-db.org/api/tsv/resolve?identifier=ADD&species=9606 > "), new File("/tmp/test.embl")); > > works as expected. > > On the other hand, please note that the String-DB guys explicitly > state: > > "Please note that we currently discourage robot access, due to the > heavy load on our server. If you require a large portion of the > interaction data which is contained in STRING, please contact one of > the authors" > (http://string.embl.de/newstring_cgi/show_robot_regulations.pl) > > So if you want to integrate this in some sort of service/agent/robot > thingy, a local copy of the database might be a good idea ! > > cheers, > -thasso > > On Dec 18, 2009, at 18:02 , jitesh dundas wrote: > > > Dear Sir/Madam, > > > > I am trying to fetch data from EMBL STRING Database (http://string.embl.de/ > > ) for a list of protein interactors. The file is attached with this > > email. > > > > On executing the code, it gives me a "version number" error. The > > same code is working fine when I fetch data from NCBI databases. > > Thus, I am trying to know what is going wrong here. > > > > I request your reply. Please let me know if you need anything else > > from my side. > > > > Regards, > > Jitesh Dundas > > > > > > > > > -- > > > > You received this message because you are subscribed to the Google > > Groups "The Java Posse" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected] > > . > > For more options, visit this group at > > http://groups.google.com/group/javaposse?hl=en > > . > > <ImportGet.jsp> > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer > Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer > Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet > Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, > Germany > > > > > > -- > > You received this message because you are subscribed to the Google > Groups "The Java Posse" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected] > . > For more options, visit this group at > http://groups.google.com/group/javaposse?hl=en > . > > > > > -- > > You received this message because you are subscribed to the Google > Groups "The Java Posse" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected] > . > For more options, visit this group at > http://groups.google.com/group/javaposse?hl=en > . > <output_File.txt><import.jsp> -- You received this message because you are subscribed to the Google Groups "The Java Posse" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/javaposse?hl=en.
