owl/trunk/dumpseq.java

import gnu.getopt.Getopt;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintStream;
import java.sql.SQLException;

import proteinstructure.Pdb;
import proteinstructure.PdbCodeNotFoundError;
import proteinstructure.PdbLoadError;
import proteinstructure.PdbasePdb;
import tools.MySQLConnection;


public class dumpseq {
        /*------------------------------ constants ------------------------------*/
        
        public static final String                      PDB_DB = "pdbase";
        public static final String                      DB_HOST = "white";                                                              
        public static final String                      DB_USER = MySQLConnection.getUserName();
        public static final String                      DB_PWD = "nieve";

        public static final String                      GAP_CHARACTER = "-";
        
        public static void main(String[] args) throws IOException {
                
                
                String help = "Usage, 3 options:\n" +
                                "1)  genGraph -i <listfile> [-o <output_dir> | -f <one_output_file> | -s] [-D <pdbase_db>] \n" +
                                "2)  genGraph -p <pdb_code> -c <chain_pdb_code> [-o <output_dir> | -f <one_output_file> | -s] [-D <pdbase_db>] \n" +
                                "Output options: -o one file per sequence, -f one file for all sequences, -s standard output"+
                                "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 pdbaseDb = PDB_DB;
                String outputDir = "";
                File oneOutputFile = null;
                boolean stdout = false;
                
                Getopt g = new Getopt("genGraph", args, "i:p:c:o:f:D:sh?");
                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 'o':
                                outputDir = g.getOptarg();
                                break;
                        case 'f':
                                oneOutputFile = new File(g.getOptarg());
                                break;                          
                        case 'D':
                                pdbaseDb = g.getOptarg();
                                break;
                        case 's':
                                stdout = true;
                                break;                          
                        case 'h':
                        case '?':
                                System.out.println(help);
                                System.exit(0);
                                break; // getopt() already printed an error
                        }
                }

                if (listfile.equals("") && pdbCodes==null){
                        System.err.println("Either a listfile or some pdb codes/chain codes must be given");
                        System.err.println(help);
                        System.exit(1);
                }
                if (!listfile.equals("") && pdbCodes!=null) {
                        System.err.println("Options -p/-c and -i 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 (!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;

                PrintStream Out = null;
                if (stdout) {
                        Out = System.out;
                } else if (oneOutputFile!=null) {
                        Out = new PrintStream(new FileOutputStream(oneOutputFile));
                } 

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

                        try {

                                Pdb pdb = new PdbasePdb(pdbCode, pdbaseDb, conn);
                                pdb.load(pdbChainCode);
                                
                                String sequence = pdb.getSequence();

                                File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+".fasta");
                                
                                if (!stdout && oneOutputFile==null) {
                                        Out = new PrintStream(new FileOutputStream(outputFile.getAbsolutePath()));
                                }
                                
                                if (!stdout) { // if output of sequence is stdout, then we don't want to print just the sequence without FASTA headers
                                        Out.println(">"+pdbCode+"_"+pdbChainCode);
                                }
                                
                                Out.println(sequence);

                                if (!stdout && oneOutputFile==null) {
                                        Out.close();
                                }
                                
                                if (!stdout) { // if output of sequence is stdout, then we don't want to print anything else to stdout
                                        System.out.println("Wrote "+pdbCode+"_"+pdbChainCode+".fasta");
                                }

                                numPdbs++;

                        } catch (PdbLoadError e) {
                                System.err.println("Error loading pdb data for " + pdbCode + pdbChainCode+", specific error: "+e.getMessage());
                        } 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());
                        }

                }

                if (!stdout && oneOutputFile!=null) {
                        Out.close();
                }
                
                // output results
                if (!stdout) { // if output of sequence is stdout, then we don't want to print anything else to stdout
                        System.out.println("Number of dumped sequences: " + numPdbs);
                }


        } 
                

}
Revision:	535
Committed:	Wed Feb 13 14:11:10 2008 UTC (16 years, 7 months ago) by duarte
File size:	5225 byte(s)
Log Message:	Added option to output to standard output
Line	File contents
1	import gnu.getopt.Getopt;
2
3	import java.io.BufferedReader;
4	import java.io.File;
5	import java.io.FileOutputStream;
6	import java.io.FileReader;
7	import java.io.IOException;
8	import java.io.PrintStream;
9	import java.sql.SQLException;
10
11	import proteinstructure.Pdb;
12	import proteinstructure.PdbCodeNotFoundError;
13	import proteinstructure.PdbLoadError;
14	import proteinstructure.PdbasePdb;
15	import tools.MySQLConnection;
16
17
18	public class dumpseq {
19	/------------------------------ constants ------------------------------/
20
21	public static final String PDB_DB = "pdbase";
22	public static final String DB_HOST = "white";
23	public static final String DB_USER = MySQLConnection.getUserName();
24	public static final String DB_PWD = "nieve";
25
26	public static final String GAP_CHARACTER = "-";
27
28	public static void main(String[] args) throws IOException {
29
30
31	String help = "Usage, 3 options:\n" +
32	"1) genGraph -i <listfile> [-o <output_dir> \| -f <one_output_file> \| -s] [-D <pdbase_db>] \n" +
33	"2) genGraph -p <pdb_code> -c <chain_pdb_code> [-o <output_dir> \| -f <one_output_file> \| -s] [-D <pdbase_db>] \n" +
34	"Output options: -o one file per sequence, -f one file for all sequences, -s standard output"+
35	"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" +
36	"If pdbase_db not specified, the default pdbase will be used\n";
37
38	String listfile = "";
39	String[] pdbCodes = null;
40	String[] pdbChainCodes = null;
41	String pdbaseDb = PDB_DB;
42	String outputDir = "";
43	File oneOutputFile = null;
44	boolean stdout = false;
45
46	Getopt g = new Getopt("genGraph", args, "i:p:c:o:f:D:sh?");
47	int c;
48	while ((c = g.getopt()) != -1) {
49	switch(c){
50	case 'i':
51	listfile = g.getOptarg();
52	break;
53	case 'p':
54	pdbCodes = g.getOptarg().split(",");
55	break;
56	case 'c':
57	pdbChainCodes = g.getOptarg().split(",");
58	break;
59	case 'o':
60	outputDir = g.getOptarg();
61	break;
62	case 'f':
63	oneOutputFile = new File(g.getOptarg());
64	break;
65	case 'D':
66	pdbaseDb = g.getOptarg();
67	break;
68	case 's':
69	stdout = true;
70	break;
71	case 'h':
72	case '?':
73	System.out.println(help);
74	System.exit(0);
75	break; // getopt() already printed an error
76	}
77	}
78
79	if (listfile.equals("") && pdbCodes==null){
80	System.err.println("Either a listfile or some pdb codes/chain codes must be given");
81	System.err.println(help);
82	System.exit(1);
83	}
84	if (!listfile.equals("") && pdbCodes!=null) {
85	System.err.println("Options -p/-c and -i are exclusive. Use only one of them");
86	System.err.println(help);
87	System.exit(1);
88	}
89
90
91	MySQLConnection conn = null;
92
93	try{
94	conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
95	} catch (Exception e) {
96	System.err.println("Error opening database connection. Exiting");
97	System.exit(1);
98	}
99
100
101
102
103	if (!listfile.equals("")) {
104	BufferedReader fpdb = new BufferedReader(new FileReader(listfile));
105	String line = "";
106	int numLines = 0;
107	fpdb.mark(100000);
108	while ((line = fpdb.readLine() ) != null ) {
109	if (line.length()>0) numLines++;
110	}
111	fpdb.reset();
112	pdbCodes = new String[numLines];
113	pdbChainCodes = new String[numLines];
114	numLines = 0;
115	while ((line = fpdb.readLine() ) != null ) {
116	pdbCodes[numLines] = line.split("\\s+")[0].toLowerCase();
117	pdbChainCodes[numLines] = line.split("\\s+")[1];
118	numLines++;
119	}
120	}
121
122	int numPdbs = 0;
123
124	PrintStream Out = null;
125	if (stdout) {
126	Out = System.out;
127	} else if (oneOutputFile!=null) {
128	Out = new PrintStream(new FileOutputStream(oneOutputFile));
129	}
130
131	for (int i=0;i<pdbCodes.length;i++) {
132	String pdbCode = pdbCodes[i];
133	String pdbChainCode = pdbChainCodes[i];
134
135	try {
136
137	Pdb pdb = new PdbasePdb(pdbCode, pdbaseDb, conn);
138	pdb.load(pdbChainCode);
139
140	String sequence = pdb.getSequence();
141
142	File outputFile = new File(outputDir,pdbCode+"_"+pdbChainCode+".fasta");
143
144	if (!stdout && oneOutputFile==null) {
145	Out = new PrintStream(new FileOutputStream(outputFile.getAbsolutePath()));
146	}
147
148	if (!stdout) { // if output of sequence is stdout, then we don't want to print just the sequence without FASTA headers
149	Out.println(">"+pdbCode+"_"+pdbChainCode);
150	}
151
152	Out.println(sequence);
153
154	if (!stdout && oneOutputFile==null) {
155	Out.close();
156	}
157
158	if (!stdout) { // if output of sequence is stdout, then we don't want to print anything else to stdout
159	System.out.println("Wrote "+pdbCode+"_"+pdbChainCode+".fasta");
160	}
161
162	numPdbs++;
163
164	} catch (PdbLoadError e) {
165	System.err.println("Error loading pdb data for " + pdbCode + pdbChainCode+", specific error: "+e.getMessage());
166	} catch (PdbCodeNotFoundError e) {
167	System.err.println("Couldn't find pdb code "+pdbCode);
168	} catch (SQLException e) {
169	System.err.println("SQL error for structure "+pdbCode+"_"+pdbChainCode+", error: "+e.getMessage());
170	}
171
172	}
173
174	if (!stdout && oneOutputFile!=null) {
175	Out.close();
176	}
177
178	// output results
179	if (!stdout) { // if output of sequence is stdout, then we don't want to print anything else to stdout
180	System.out.println("Number of dumped sequences: " + numPdbs);
181	}
182
183
184	}
185
186
187	}