runner/compbio/runner/_impl/PSIBlast.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.runner._impl;\r
  19 \r
  20 import static compbio.runner._impl.BlastParameters.parAlView;\r
  21 import static compbio.runner._impl.BlastParameters.parDatabase;\r
  22 import static compbio.runner._impl.BlastParameters.parDel;\r
  23 import static compbio.runner._impl.BlastParameters.parEvalue;\r
  24 import static compbio.runner._impl.BlastParameters.parInput;\r
  25 import static compbio.runner._impl.BlastParameters.parOutput;\r
  26 \r
  27 import java.io.File;\r
  28 import java.util.Arrays;\r
  29 import java.util.List;\r
  30 \r
  31 import compbio.runner._SkeletalCommandBuilder;\r
  32 \r
  33 /*\r
  34  * TODO look at how a command can be build with an argument list\r
  35  */\r
  36 public class PSIBlast extends _SkeletalCommandBuilder {\r
  37 \r
  38         private static final String command = "blastpgp";\r
  39 \r
  40         enum blastType {\r
  41                 blastp, tbastn, blastn\r
  42         }\r
  43 \r
  44         enum dataBase {\r
  45                 pdb\r
  46         }\r
  47 \r
  48         static double default_evalue = 0.001d;\r
  49         static final String parBlastType = "-p";\r
  50 \r
  51         private final String workDirectory;\r
  52 \r
  53         public PSIBlast(String workDirectory) {\r
  54                 this.workDirectory = workDirectory;\r
  55         }\r
  56 \r
  57         // Resulting command:\r
  58         // TODO lease note that the location seem to be different for 64 bit nodes\r
  59         // fc_gpfs/gjb_lab/www-refine/bin/blast_32bit/blast-2.2.17/bin/blastpgp -i\r
  60         // $input -d $dbnam -o $output_dir/$outfile.psiblastout.$clus -j $iterations\r
  61         // -Q $output_dir/$outfile.PSImatrix.$clus -m $mo\r
  62 \r
  63         // BlastAll\r
  64         // //fc_gpfs/gjb_lab/www-refine/bin/blast_32bit/blast-2.2.17/bin/blastall -p\r
  65         // blastp -i $input -d $dbnam -e $evalue -m 9 -o $outfile\r
  66 \r
  67         String getCommand(blastType btype, dataBase database, String input,\r
  68                         String output) {\r
  69                 return Environment.getBlastBinDir() + command + parDel + parBlastType\r
  70                                 + blastType.blastp + parDel + parInput + input + parDel\r
  71                                 + parDatabase + Environment.getBlastDatabasesDir() + database\r
  72                                 + parDel + parEvalue + default_evalue + parAlView + parOutput\r
  73                                 + output;\r
  74         }\r
  75 \r
  76         String getFullTestCommand(String test_input, String test_outfile) {\r
  77                 return Environment.getBlastBinDir() + command + parDel + parBlastType\r
  78                                 + blastType.blastp + parDel + parInput + test_input + parDel\r
  79                                 + parDatabase + Environment.getBlastDatabasesDir()\r
  80                                 + dataBase.pdb + parDel + parEvalue + default_evalue\r
  81                                 + parAlView + parOutput + test_outfile;\r
  82         }\r
  83 \r
  84         static String getTestCommand() {\r
  85                 return Environment.getBlastBinDir() + command;\r
  86         }\r
  87 \r
  88         static List<String> getTestArgs() {\r
  89                 return Arrays\r
  90                                 .asList(new String[] {\r
  91                                                 parBlastType + blastType.blastp,\r
  92                                                 parDatabase + Environment.getBlastDatabasesDir()\r
  93                                                                 + dataBase.pdb, parEvalue + default_evalue,\r
  94                                                 parAlView });\r
  95         }\r
  96 \r
  97         public boolean removeOutput(String outfile) {\r
  98                 File out = new File(outfile);\r
  99                 if (out.exists()) {\r
 100                         if (out.canWrite()) {\r
 101                                 return out.delete();\r
 102                         }\r
 103                 }\r
 104                 return false;\r
 105         }\r
 106 \r
 107         public String getCommand(ExecProvider provider) {\r
 108                 return Environment.getBlastBinDir() + command;\r
 109         }\r
 110 \r
 111         public String getCommandName() {\r
 112                 return command;\r
 113         }\r
 114 \r
 115         @Override\r
 116         public List<String> getCreatedFiles() {\r
 117                 // TODO Auto-generated method stub\r
 118                 return null;\r
 119         }\r
 120 \r
 121         @Override\r
 122         public String getInput() {\r
 123                 // TODO Auto-generated method stub\r
 124                 return null;\r
 125         }\r
 126 \r
 127 }\r