owl/trunk/genDbGraph.java

import gnu.getopt.Getopt;

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.sql.SQLException;


import proteinstructure.Graph;
import proteinstructure.Pdb;
import proteinstructure.PdbChainCodeNotFoundError;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbaseInconsistencyError;
import proteinstructure.PdbasePdb;
import proteinstructure.PdbfileFormatError;
import proteinstructure.PdbfilePdb;
import tools.MySQLConnection;


public class genDbGraph {
        /*------------------------------ constants ------------------------------*/
        
        public static final String                      PDB_DB = "pdbase";
        public static final String                      DB_HOST = "white";                                                              
        public static final String                      DB_USER = getUserName();
        public static final String                      DB_PWD = "nieve";
        public static final String                      DSSP_EXE = "/project/StruPPi/bin/dssp";
        public static final String                      DSSP_PARAMS = "--";

        //public static double                  cutoff = 4.2;
        //public static String                  edgeType = "ALL";
        
        /*---------------------------- private methods --------------------------*/
        /** 
         * Get user name from operating system (for use as database username). 
         * */
        private static String getUserName() {
                String user = null;
                user = System.getProperty("user.name");
                if(user == null) {
                        System.err.println("Could not get user name from operating system.");
                }
                return user;
        }
        
        public static void main(String[] args) throws IOException {
                
                
                String help = "Usage, 3 options:\n" +
                                "1)  genDbGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_db> [-D <pdbase_db>] \n" +
                                "2)  genDbGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_db> [-D <pdbase_db>] \n" +
                                "3)  genDbGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_db> \n" +
                                "In case 2) also a list of comma separated pdb codes and chain codes can be specified, e.g. -p 1bxy,1jos -c A,A\n" +
                                "If pdbase_db not specified, the default pdbase will be used\n"; 

                String listfile = "";
                String[] pdbCodes = null;
                String[] pdbChainCodes = null;
                String pdbfile = "";
                String pdbaseDb = PDB_DB;
                String edgeType = "";
                double cutoff = 0.0;
                String outputDb = "";
                
                Getopt g = new Getopt("genDbGraph", args, "i:p:c:f:d:t:o:D:h?");
                int c;
                while ((c = g.getopt()) != -1) {
                        switch(c){
                        case 'i':
                                listfile = g.getOptarg();
                                break;
                        case 'p':
                                pdbCodes = g.getOptarg().split(",");
                                break;
                        case 'c':
                                pdbChainCodes = g.getOptarg().split(",");
                                break;
                        case 'f':
                                pdbfile = g.getOptarg();
                                break;
                        case 'd':
                                cutoff = Double.valueOf(g.getOptarg());
                                break;
                        case 't':
                                edgeType = g.getOptarg();
                                break;
                        case 'o':
                                outputDb = g.getOptarg();
                                break;
                        case 'D':
                                pdbaseDb = g.getOptarg();
                                break;
                        case 'h':
                        case '?':
                                System.out.println(help);
                                System.exit(0);
                                break; // getopt() already printed an error
                        }
                }

                if (outputDb.equals("") || edgeType.equals("") || cutoff==0.0) {
                        System.err.println("Some missing option");
                        System.err.println(help);
                        System.exit(1);
                }
                if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
                        System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given");
                        System.err.println(help);
                        System.exit(1);
                }
                if ((!listfile.equals("") && pdbCodes!=null) || (!listfile.equals("") && !pdbfile.equals("")) || (pdbCodes!=null && !pdbfile.equals(""))) {
                        System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them");
                        System.err.println(help);
                        System.exit(1);                 
                }

                
                MySQLConnection conn = null;            

                try{
                        conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
                } catch (Exception e) {
                        System.err.println("Error opening database connection. Exiting");
                        System.exit(1);
                }
                
                
                if (pdbfile.equals("")){
                        
                        if (!listfile.equals("")) {                     
                                BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
                                String line = "";
                                int numLines = 0;
                                fpdb.mark(100000);
                                while ((line = fpdb.readLine() ) != null ) {
                                        numLines++;
                                }
                                fpdb.reset();
                                pdbCodes = new String[numLines];
                                pdbChainCodes = new String[numLines];
                                numLines = 0;
                                while ((line = fpdb.readLine() ) != null ) {
                                        pdbCodes[numLines] = line.split("\\s")[0].toLowerCase();
                                        pdbChainCodes[numLines] = line.split("\\s")[1];
                                        numLines++;
                                }
                        }

                        int numPdbs = 0;

                        for (int i=0;i<pdbCodes.length;i++) {
                                String pdbCode = pdbCodes[i];
                                String pdbChainCode = pdbChainCodes[i];

                                if(pdbChainCode == null) {
                                        pdbChainCode = "NULL";
                                }

                                
                                try {
                                        Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);

                                        // get graph
                                        Graph graph = pdb.get_graph(edgeType, cutoff);

                                        graph.write_graph_to_db(conn,outputDb);

                                        System.out.println(pdbCode+"_"+pdbChainCode);
                                        numPdbs++;
                                        
                                } catch (PdbaseInconsistencyError e) {
                                        System.err.println("Inconsistency in " + pdbCode + pdbChainCode);
                                } catch (PdbCodeNotFoundError e) {
                                        System.err.println("Couldn't find pdb code "+pdbCode);
                                } catch (SQLException e) {
                                        e.printStackTrace();
                                } catch (PdbChainCodeNotFoundError e) {
                                        System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode);
                                }

                        }

                        // output results
                        System.out.println("Number of structures loaded successfully: " + numPdbs);


                } else {
                        String pdbChainCode = pdbChainCodes[0];
                        try {
                                Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
                                if (!pdb.hasSecondaryStructure()) {
                                        pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
                                }
                                Graph graph = pdb.get_graph(edgeType, cutoff);
                                try {
                                        graph.write_graph_to_db(conn, outputDb);
                                        System.out.println("Loaded to database graph for file "+pdbfile);
                                } catch (SQLException e) {
                                        e.printStackTrace();
                                }
                                
                        } catch (PdbfileFormatError e) {
                                System.err.println("pdb file "+pdbfile+" doesn't have right format");
                        } catch (PdbChainCodeNotFoundError e) {
                                System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile);        
                        }
                }
        }

}
Revision:	277
Committed:	Tue Aug 14 10:54:24 2007 UTC (17 years, 1 month ago) by duarte
File size:	6189 byte(s)
Log Message:	New script genGraph (generates graph to files) Better error messages in both
Line	User	Rev	File contents
1	duarte	264	import gnu.getopt.Getopt;
2
3			import java.io.BufferedReader;
4			import java.io.FileReader;
5			import java.io.IOException;
6			import java.sql.SQLException;
7
8
9			import proteinstructure.Graph;
10			import proteinstructure.Pdb;
11			import proteinstructure.PdbChainCodeNotFoundError;
12			import proteinstructure.PdbCodeNotFoundError;
13			import proteinstructure.PdbaseInconsistencyError;
14			import proteinstructure.PdbasePdb;
15			import proteinstructure.PdbfileFormatError;
16			import proteinstructure.PdbfilePdb;
17			import tools.MySQLConnection;
18
19
20			public class genDbGraph {
21			/------------------------------ constants ------------------------------/
22
23			public static final String PDB_DB = "pdbase";
24			public static final String DB_HOST = "white";
25			public static final String DB_USER = getUserName();
26			public static final String DB_PWD = "nieve";
27			public static final String DSSP_EXE = "/project/StruPPi/bin/dssp";
28			public static final String DSSP_PARAMS = "--";
29
30			//public static double cutoff = 4.2;
31			//public static String edgeType = "ALL";
32
33			/---------------------------- private methods --------------------------/
34			/**
35			* Get user name from operating system (for use as database username).
36			* */
37			private static String getUserName() {
38			String user = null;
39			user = System.getProperty("user.name");
40			if(user == null) {
41			System.err.println("Could not get user name from operating system.");
42			}
43			return user;
44			}
45
46			public static void main(String[] args) throws IOException {
47
48
49			String help = "Usage, 3 options:\n" +
50			"1) genDbGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_db> [-D <pdbase_db>] \n" +
51			"2) genDbGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_db> [-D <pdbase_db>] \n" +
52			"3) genDbGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_db> \n" +
53			"In case 2) also a list of comma separated pdb codes and chain codes can be specified, e.g. -p 1bxy,1jos -c A,A\n" +
54			"If pdbase_db not specified, the default pdbase will be used\n";
55
56			String listfile = "";
57			String[] pdbCodes = null;
58			String[] pdbChainCodes = null;
59			String pdbfile = "";
60			String pdbaseDb = PDB_DB;
61			String edgeType = "";
62			double cutoff = 0.0;
63			String outputDb = "";
64
65			Getopt g = new Getopt("genDbGraph", args, "i:p:c:f:d:t:o:D:h?");
66			int c;
67			while ((c = g.getopt()) != -1) {
68			switch(c){
69			case 'i':
70			listfile = g.getOptarg();
71			break;
72			case 'p':
73			pdbCodes = g.getOptarg().split(",");
74			break;
75			case 'c':
76			pdbChainCodes = g.getOptarg().split(",");
77			break;
78			case 'f':
79			pdbfile = g.getOptarg();
80			break;
81			case 'd':
82			cutoff = Double.valueOf(g.getOptarg());
83			break;
84			case 't':
85			edgeType = g.getOptarg();
86			break;
87			case 'o':
88			outputDb = g.getOptarg();
89			break;
90			case 'D':
91			pdbaseDb = g.getOptarg();
92			break;
93			case 'h':
94			case '?':
95			System.out.println(help);
96			System.exit(0);
97			break; // getopt() already printed an error
98			}
99			}
100
101			if (outputDb.equals("") \|\| edgeType.equals("") \|\| cutoff==0.0) {
102			System.err.println("Some missing option");
103			System.err.println(help);
104			System.exit(1);
105			}
106			if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
107			System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given");
108			System.err.println(help);
109			System.exit(1);
110			}
111			if ((!listfile.equals("") && pdbCodes!=null) \|\| (!listfile.equals("") && !pdbfile.equals("")) \|\| (pdbCodes!=null && !pdbfile.equals(""))) {
112			System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them");
113			System.err.println(help);
114			System.exit(1);
115			}
116
117
118			MySQLConnection conn = null;
119
120			try{
121			conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
122			} catch (Exception e) {
123			System.err.println("Error opening database connection. Exiting");
124			System.exit(1);
125			}
126
127
128			if (pdbfile.equals("")){
129
130			if (!listfile.equals("")) {
131			BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
132			String line = "";
133			int numLines = 0;
134			fpdb.mark(100000);
135			while ((line = fpdb.readLine() ) != null ) {
136			numLines++;
137			}
138			fpdb.reset();
139			pdbCodes = new String[numLines];
140			pdbChainCodes = new String[numLines];
141			numLines = 0;
142			while ((line = fpdb.readLine() ) != null ) {
143			pdbCodes[numLines] = line.split("\\s")[0].toLowerCase();
144			pdbChainCodes[numLines] = line.split("\\s")[1];
145			numLines++;
146			}
147			}
148
149			int numPdbs = 0;
150
151			for (int i=0;i<pdbCodes.length;i++) {
152			String pdbCode = pdbCodes[i];
153			String pdbChainCode = pdbChainCodes[i];
154
155			if(pdbChainCode == null) {
156			pdbChainCode = "NULL";
157			}
158
159	duarte	277
160	duarte	264	try {
161	duarte	277	Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);
162	duarte	264
163			// get graph
164			Graph graph = pdb.get_graph(edgeType, cutoff);
165
166			graph.write_graph_to_db(conn,outputDb);
167
168			System.out.println(pdbCode+"_"+pdbChainCode);
169	duarte	277	numPdbs++;
170
171	duarte	264	} catch (PdbaseInconsistencyError e) {
172	duarte	277	System.err.println("Inconsistency in " + pdbCode + pdbChainCode);
173	duarte	264	} catch (PdbCodeNotFoundError e) {
174	duarte	277	System.err.println("Couldn't find pdb code "+pdbCode);
175	duarte	264	} catch (SQLException e) {
176			e.printStackTrace();
177			} catch (PdbChainCodeNotFoundError e) {
178	duarte	277	System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode);
179	duarte	264	}
180
181			}
182
183			// output results
184	duarte	277	System.out.println("Number of structures loaded successfully: " + numPdbs);
185	duarte	264
186
187			} else {
188			String pdbChainCode = pdbChainCodes[0];
189			try {
190			Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
191			if (!pdb.hasSecondaryStructure()) {
192			pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
193			}
194			Graph graph = pdb.get_graph(edgeType, cutoff);
195			try {
196			graph.write_graph_to_db(conn, outputDb);
197			System.out.println("Loaded to database graph for file "+pdbfile);
198			} catch (SQLException e) {
199			e.printStackTrace();
200			}
201
202			} catch (PdbfileFormatError e) {
203			System.err.println("pdb file "+pdbfile+" doesn't have right format");
204			} catch (PdbChainCodeNotFoundError e) {
205			System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile);
206			}
207			}
208			}
209
210			}