[Biojava-l] Run blast on multiple databases

[Laurence Hummel]

Hi,
I want to run blastall on several databases, so I run it with -d 
"dbName1 dbName2"...
This work well if I launch the command line in a terminal, but not if I 
launch it from my java program...
It seems like the "" are not reconized.
Here is what I've done :

         Process blastRun;
         String pOption, dOption, oOption, iOption, eOption, tOption, 
blastCommandLine, line;
         BufferedReader errorBuff;
         File outFile;

         try {
             pOption = " -p " + program;
             tOption = " -T"; // out file in html format
             dOption = " -d \"" + db + "\"";
             iOption = " -i " + query;
             eOption = " -e " + eValue;
             oOption = " -o " + outFilePath;

             blastCommandLine = exePath + pOption + dOption + tOption + 
iOption + eOption + oOption;

             System.out.println("\nblastcommandLine = " + 
blastCommandLine);

             // Call external blastall programm
             blastRun = Runtime.getRuntime().exec(blastCommandLine);

             // Catch blast error
             System.out.println("\nErrorStream = " + 
blastRun.getErrorStream().read());
             errorBuff = new BufferedReader(new 
InputStreamReader(blastRun.getErrorStream()));
             System.out.println("\nerrorBuff = ");
             while ((line = errorBuff.readLine()) != null) {
                 System.out.println(line);
             }
             System.out.println("\nOutputStream = " + 
blastRun.getOutputStream());

         } catch (IOException ex) {
             System.out.println("BLAST NOT RUN");
             System.out.println("IOException : " + ex.toString());

         }


And here is the error :

blastcommandLine = /Applications/blast/blastall  -p blastp -d "db1 db2" 
-T -i query.faa -e 10.0 -o /out.html

ErrorStream = 91

errorBuff =
blastall] ERROR: Arguments must start with '-' (the offending argument 
#5 was: db2"')

OutputStream = java.io.BufferedOutputStream at 629355

The exactly same command line copy/pasted in a terminal works very 
well...

Is someone has an idea?

Laurence


--
Laurence HUMMEL
Génopole - Plate-Forme 4 "Intégration et Analyse Génomiques"
Institut Pasteur
28 rue du docteur Roux - 75015 PARIS
Tel : 01.44.38.95.36
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