owl/trunk/genGraph.java

import gnu.getopt.Getopt;

import java.io.BufferedReader;
import java.io.File;
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 genGraph {
        /*------------------------------ 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)  genGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
                                "2)  genGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
                                "3)  genGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> \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 outputDir = "";
                
                Getopt g = new Getopt("genGraph", 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':
                                outputDir = 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 (outputDir.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 ) {
                                        if (line.length()>0) 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];

                                try {
                                        
                                        long start = System.currentTimeMillis();
                                        
                                        Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);

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

                                        File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
                                        graph.write_graph_to_file(outputFile.getAbsolutePath());

                                        long end = System.currentTimeMillis();
                                        double time = (double) (end -start)/1000;

                                        System.out.println("Wrote "+outputFile.getAbsolutePath());
                                        System.out.printf("%5.3f s\n",time);
                                        
                                        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) {
                                        System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
                                } 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 done 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);

                                File outputFile = new File(outputDir,pdb.getPdbCode()+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
                                graph.write_graph_to_file(outputFile.getAbsolutePath());
                                System.out.println("Wrote graph file "+outputFile.getAbsolutePath()+" from pdb file "+pdbfile);
                                
                        } 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:	285
Committed:	Thu Aug 16 15:10:11 2007 UTC (17 years, 1 month ago) by duarte
File size:	6642 byte(s)
Log Message:	Fixed a few bugs in reading of list file Better output and error messages
Line	File contents
1	import gnu.getopt.Getopt;
2
3	import java.io.BufferedReader;
4	import java.io.File;
5	import java.io.FileReader;
6	import java.io.IOException;
7	import java.sql.SQLException;
8
9
10	import proteinstructure.Graph;
11	import proteinstructure.Pdb;
12	import proteinstructure.PdbChainCodeNotFoundError;
13	import proteinstructure.PdbCodeNotFoundError;
14	import proteinstructure.PdbaseInconsistencyError;
15	import proteinstructure.PdbasePdb;
16	import proteinstructure.PdbfileFormatError;
17	import proteinstructure.PdbfilePdb;
18	import tools.MySQLConnection;
19
20
21	public class genGraph {
22	/------------------------------ constants ------------------------------/
23
24	public static final String PDB_DB = "pdbase";
25	public static final String DB_HOST = "white";
26	public static final String DB_USER = getUserName();
27	public static final String DB_PWD = "nieve";
28	public static final String DSSP_EXE = "/project/StruPPi/bin/dssp";
29	public static final String DSSP_PARAMS = "--";
30
31	//public static double cutoff = 4.2;
32	//public static String edgeType = "ALL";
33
34	/---------------------------- private methods --------------------------/
35	/**
36	* Get user name from operating system (for use as database username).
37	* */
38	private static String getUserName() {
39	String user = null;
40	user = System.getProperty("user.name");
41	if(user == null) {
42	System.err.println("Could not get user name from operating system.");
43	}
44	return user;
45	}
46
47	public static void main(String[] args) throws IOException {
48
49
50	String help = "Usage, 3 options:\n" +
51	"1) genGraph -i <listfile> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
52	"2) genGraph -p <pdb_code> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> [-D <pdbase_db>] \n" +
53	"3) genGraph -f <pdbfile> -c <chain_pdb_code> -d <distance_cutoff> -t <contact_type> -o <output_dir> \n" +
54	"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" +
55	"If pdbase_db not specified, the default pdbase will be used\n";
56
57	String listfile = "";
58	String[] pdbCodes = null;
59	String[] pdbChainCodes = null;
60	String pdbfile = "";
61	String pdbaseDb = PDB_DB;
62	String edgeType = "";
63	double cutoff = 0.0;
64	String outputDir = "";
65
66	Getopt g = new Getopt("genGraph", args, "i:p:c:f:d:t:o:D:h?");
67	int c;
68	while ((c = g.getopt()) != -1) {
69	switch(c){
70	case 'i':
71	listfile = g.getOptarg();
72	break;
73	case 'p':
74	pdbCodes = g.getOptarg().split(",");
75	break;
76	case 'c':
77	pdbChainCodes = g.getOptarg().split(",");
78	break;
79	case 'f':
80	pdbfile = g.getOptarg();
81	break;
82	case 'd':
83	cutoff = Double.valueOf(g.getOptarg());
84	break;
85	case 't':
86	edgeType = g.getOptarg();
87	break;
88	case 'o':
89	outputDir = g.getOptarg();
90	break;
91	case 'D':
92	pdbaseDb = g.getOptarg();
93	break;
94	case 'h':
95	case '?':
96	System.out.println(help);
97	System.exit(0);
98	break; // getopt() already printed an error
99	}
100	}
101
102	if (outputDir.equals("") \|\| edgeType.equals("") \|\| cutoff==0.0) {
103	System.err.println("Some missing option");
104	System.err.println(help);
105	System.exit(1);
106	}
107	if (listfile.equals("") && pdbCodes==null && pdbfile.equals("")){
108	System.err.println("Either a listfile, some pdb codes/chain codes or a pdbfile must be given");
109	System.err.println(help);
110	System.exit(1);
111	}
112	if ((!listfile.equals("") && pdbCodes!=null) \|\| (!listfile.equals("") && !pdbfile.equals("")) \|\| (pdbCodes!=null && !pdbfile.equals(""))) {
113	System.err.println("Options -p/-c, -i and -f/-c are exclusive. Use only one of them");
114	System.err.println(help);
115	System.exit(1);
116	}
117
118
119	MySQLConnection conn = null;
120
121	try{
122	conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
123	} catch (Exception e) {
124	System.err.println("Error opening database connection. Exiting");
125	System.exit(1);
126	}
127
128
129	if (pdbfile.equals("")){
130
131	if (!listfile.equals("")) {
132	BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
133	String line = "";
134	int numLines = 0;
135	fpdb.mark(100000);
136	while ((line = fpdb.readLine() ) != null ) {
137	if (line.length()>0) numLines++;
138	}
139	fpdb.reset();
140	pdbCodes = new String[numLines];
141	pdbChainCodes = new String[numLines];
142	numLines = 0;
143	while ((line = fpdb.readLine() ) != null ) {
144	pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
145	pdbChainCodes[numLines] = line.split("\\s+")[1];
146	numLines++;
147	}
148	}
149
150	int numPdbs = 0;
151
152	for (int i=0;i<pdbCodes.length;i++) {
153	String pdbCode = pdbCodes[i];
154	String pdbChainCode = pdbChainCodes[i];
155
156	try {
157
158	long start = System.currentTimeMillis();
159
160	Pdb pdb = new PdbasePdb(pdbCode, pdbChainCode, pdbaseDb, conn);
161
162	// get graph
163	Graph graph = pdb.get_graph(edgeType, cutoff);
164
165	File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
166	graph.write_graph_to_file(outputFile.getAbsolutePath());
167
168	long end = System.currentTimeMillis();
169	double time = (double) (end -start)/1000;
170
171	System.out.println("Wrote "+outputFile.getAbsolutePath());
172	System.out.printf("%5.3f s\n",time);
173
174	numPdbs++;
175
176	} catch (PdbaseInconsistencyError e) {
177	System.err.println("Inconsistency in " + pdbCode + pdbChainCode);
178	} catch (PdbCodeNotFoundError e) {
179	System.err.println("Couldn't find pdb code "+pdbCode);
180	} catch (SQLException e) {
181	System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
182	} catch (PdbChainCodeNotFoundError e) {
183	System.err.println("Couldn't find pdb chain code "+pdbChainCode+" for pdb code "+pdbCode);
184	}
185
186	}
187
188	// output results
189	System.out.println("Number of structures done successfully: " + numPdbs);
190
191
192	} else {
193	String pdbChainCode = pdbChainCodes[0];
194	try {
195	Pdb pdb = new PdbfilePdb(pdbfile,pdbChainCode);
196	if (!pdb.hasSecondaryStructure()) {
197	pdb.runDssp(DSSP_EXE, DSSP_PARAMS);
198	}
199	Graph graph = pdb.get_graph(edgeType, cutoff);
200
201	File outputFile = new File(outputDir,pdb.getPdbCode()+"_"+pdbChainCode+"_"+edgeType+"_"+cutoff+".graph");
202	graph.write_graph_to_file(outputFile.getAbsolutePath());
203	System.out.println("Wrote graph file "+outputFile.getAbsolutePath()+" from pdb file "+pdbfile);
204
205	} catch (PdbfileFormatError e) {
206	System.err.println("pdb file "+pdbfile+" doesn't have right format");
207	} catch (PdbChainCodeNotFoundError e) {
208	System.err.println("chain code "+pdbChainCode+" wasn't found in file "+pdbfile);
209	}
210	}
211	}
212
213	}