owl/trunk/testGraphAverager.java

import java.io.*;
import java.util.*;
import proteinstructure.*;

public class testGraphAverager {

        /**
         * @param args
         */
        public static void main(String[] args) {
                // Plan:
                // use getopt to parse the following parameters
                // - original structure (optional, for benchmarking)
                // - file with list of structures for averaging (required)
                // - contact type & distance cutoff (both required)
                // - consensus edge threshold (defaults to 0.5?)
                // - run tinker or not
                // - parameters for tinker model picking (optional)
                // - number of tinker models to output (only if run tinker is set, defaults to one)
                // - output benchmark result (graph comparison or structure comparison, only if original structure is specified)
                // - output file for resulting graph (optional)
                
                // take pdb files from command line (later: use getopt)
                // create trivial alignment (check alignment)
                // create graphAverager
                // create consensus graph
                // compare with graph for native structure (first argument)
                
                // do tinker reconstruction
                // compare with native structure
                
                // benchmarking:
                // - use score of best model vs. native (either graph based or structure based)
                // - use matlab to optimize input parameters
                // - create matlab executable for optimizing command line parameters:
                //   * specify command line to be run and constant parameters
                //   * specify parameter ranges to be optimized (discrete numerical, continuous numerical with steps, discrete set)
                //   * specify regexp to parse result from output (stdout or file)
                //   * specify optimization procedure (use default matlab ones, e.g. each parameter separate, genetic algorithm, simul. annealing, ...)
                //   * specify convergence threshold or timeout
                //   * run on cluster?
                
                
                // read command line parameters
                if(args.length < 4) {
                        System.out.println("Usage: testGraphAverager <targetPdbFile> <ChainCode> <ListOfPredictionFiles> <edgeThreshold>");
                        System.exit(1);
                }
                
                File targetFile = new File(args[0]);
                File listFile = new File(args[2]);
                String chainCode = args[1];
                String thresholdStr = args[3];
                Pdb target = null;
                Graph targetGraph = null;
                Vector<String> modelFileNames = new Vector<String>();
                Vector<Graph> models = new Vector<Graph>();
                String contactType = "Cb";
                double distCutoff = 7.0;
                double graphAveragingThreshold = Double.parseDouble(thresholdStr); 
                
                if(!targetFile.canRead()) {
                        System.err.println("Can not read from file " + targetFile.getAbsolutePath());
                        System.exit(1);
                }
                if(!listFile.canRead()) {
                        System.err.println("Can not read from file " + listFile.getAbsolutePath());
                        System.exit(1);
                }
                
                // read input files
                try {
                        target = new PdbfilePdb(targetFile.getAbsolutePath(), chainCode);
                        targetGraph = target.get_graph(contactType, distCutoff);
                } catch(PdbChainCodeNotFoundError e) {
                        System.err.println("Chain code " + chainCode + " not found in file " + targetFile.getAbsolutePath());
                        System.exit(1);
                } catch(PdbfileFormatError e) {
                        System.err.println("Formating error in file " + targetFile.getAbsolutePath());  
                        System.exit(1);
                } catch (FileNotFoundException e) {
                        System.err.println("File " + targetFile.getAbsolutePath() + " not found");      
                        System.exit(1);                 
                } catch(IOException e) {
                        System.err.println("Error reading from file " + targetFile.getAbsolutePath());  
                        System.exit(1);                         
                }
                
                try {
                        BufferedReader in = new BufferedReader(new FileReader(listFile));
                        String line;
                        File file;
                        Pdb pdb;
                        Graph graph;
                        while ((line =  in.readLine()  ) != null) {
                                file = new File(line);
                                if(!file.canRead()) {
                                        System.err.println("File " + line + " not found.");
                                        System.exit(1);
                                } else {
                                        modelFileNames.add(line);
                                        try {
                                                pdb = new PdbfilePdb(file.getAbsolutePath(),Pdb.NULL_CHAIN_CODE);
                                                graph = pdb.get_graph(contactType, distCutoff);
                                                models.add(graph);
                                        } catch(PdbChainCodeNotFoundError e) {
                                                System.err.println("Chain code " + chainCode + " not found in file " + file.getAbsolutePath());
                                                System.exit(1);
                                        } catch(PdbfileFormatError e) {
                                                System.err.println("Formating error in file " + file.getAbsolutePath());        
                                                System.exit(1);
                                        } catch (FileNotFoundException e) {
                                                System.err.println("File " + file.getAbsolutePath() + " not found");    
                                                System.exit(1);                 
                                        } catch(IOException e) {
                                                System.err.println("Error reading from file " + file.getAbsolutePath());        
                                                System.exit(1);                         
                                        }
                                }
                        }
                        in.close();

                } catch(FileNotFoundException e) {
                        System.err.println("File " + listFile.getAbsolutePath() + " not found.");
                        System.exit(1);
                } catch(IOException e) {
                        System.err.println("Error reading from file " + listFile.getAbsolutePath());
                        System.exit(1);
                }
                
                // create alignment
                TreeMap<String,String> sequences = new TreeMap<String, String>();
                TreeMap<String, Graph> templateGraphs = new TreeMap<String, Graph>();
                sequences.put(targetFile.getAbsolutePath(), targetGraph.getSequence());
                for(int i=0; i < models.size(); i++) {
                        sequences.put(modelFileNames.get(i), models.get(i).getSequence());
                        templateGraphs.put(modelFileNames.get(i), models.get(i));
                }
                Alignment al = new Alignment(sequences);
                
                // create GraphAverager
                GraphAverager grav = new GraphAverager(targetGraph.getSequence(), al, templateGraphs, targetFile.getAbsolutePath());
                Graph resultGraph = grav.doAveraging(graphAveragingThreshold);
                
                // compare prediction with target
                PredEval eval = resultGraph.evaluatePrediction(targetGraph);
                eval.print();
                
                // write result graph to file
                try {
                        resultGraph.write_graph_to_file("predictedGraph.cm");
                } catch (IOException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                }
                
        }
}
Revision:	351
Committed:	Thu Oct 11 12:43:54 2007 UTC (17 years, 4 months ago) by stehr
File size:	5786 byte(s)
Log Message:	added some test programs to default package
Line	File contents
1	import java.io.*;
2	import java.util.*;
3	import proteinstructure.*;
4
5	public class testGraphAverager {
6
7	/**
8	* @param args
9	*/
10	public static void main(String[] args) {
11	// Plan:
12	// use getopt to parse the following parameters
13	// - original structure (optional, for benchmarking)
14	// - file with list of structures for averaging (required)
15	// - contact type & distance cutoff (both required)
16	// - consensus edge threshold (defaults to 0.5?)
17	// - run tinker or not
18	// - parameters for tinker model picking (optional)
19	// - number of tinker models to output (only if run tinker is set, defaults to one)
20	// - output benchmark result (graph comparison or structure comparison, only if original structure is specified)
21	// - output file for resulting graph (optional)
22
23	// take pdb files from command line (later: use getopt)
24	// create trivial alignment (check alignment)
25	// create graphAverager
26	// create consensus graph
27	// compare with graph for native structure (first argument)
28
29	// do tinker reconstruction
30	// compare with native structure
31
32	// benchmarking:
33	// - use score of best model vs. native (either graph based or structure based)
34	// - use matlab to optimize input parameters
35	// - create matlab executable for optimizing command line parameters:
36	// * specify command line to be run and constant parameters
37	// * specify parameter ranges to be optimized (discrete numerical, continuous numerical with steps, discrete set)
38	// * specify regexp to parse result from output (stdout or file)
39	// * specify optimization procedure (use default matlab ones, e.g. each parameter separate, genetic algorithm, simul. annealing, ...)
40	// * specify convergence threshold or timeout
41	// * run on cluster?
42
43
44	// read command line parameters
45	if(args.length < 4) {
46	System.out.println("Usage: testGraphAverager <targetPdbFile> <ChainCode> <ListOfPredictionFiles> <edgeThreshold>");
47	System.exit(1);
48	}
49
50	File targetFile = new File(args[0]);
51	File listFile = new File(args[2]);
52	String chainCode = args[1];
53	String thresholdStr = args[3];
54	Pdb target = null;
55	Graph targetGraph = null;
56	Vector<String> modelFileNames = new Vector<String>();
57	Vector<Graph> models = new Vector<Graph>();
58	String contactType = "Cb";
59	double distCutoff = 7.0;
60	double graphAveragingThreshold = Double.parseDouble(thresholdStr);
61
62	if(!targetFile.canRead()) {
63	System.err.println("Can not read from file " + targetFile.getAbsolutePath());
64	System.exit(1);
65	}
66	if(!listFile.canRead()) {
67	System.err.println("Can not read from file " + listFile.getAbsolutePath());
68	System.exit(1);
69	}
70
71	// read input files
72	try {
73	target = new PdbfilePdb(targetFile.getAbsolutePath(), chainCode);
74	targetGraph = target.get_graph(contactType, distCutoff);
75	} catch(PdbChainCodeNotFoundError e) {
76	System.err.println("Chain code " + chainCode + " not found in file " + targetFile.getAbsolutePath());
77	System.exit(1);
78	} catch(PdbfileFormatError e) {
79	System.err.println("Formating error in file " + targetFile.getAbsolutePath());
80	System.exit(1);
81	} catch (FileNotFoundException e) {
82	System.err.println("File " + targetFile.getAbsolutePath() + " not found");
83	System.exit(1);
84	} catch(IOException e) {
85	System.err.println("Error reading from file " + targetFile.getAbsolutePath());
86	System.exit(1);
87	}
88
89	try {
90	BufferedReader in = new BufferedReader(new FileReader(listFile));
91	String line;
92	File file;
93	Pdb pdb;
94	Graph graph;
95	while ((line = in.readLine() ) != null) {
96	file = new File(line);
97	if(!file.canRead()) {
98	System.err.println("File " + line + " not found.");
99	System.exit(1);
100	} else {
101	modelFileNames.add(line);
102	try {
103	pdb = new PdbfilePdb(file.getAbsolutePath(),Pdb.NULL_CHAIN_CODE);
104	graph = pdb.get_graph(contactType, distCutoff);
105	models.add(graph);
106	} catch(PdbChainCodeNotFoundError e) {
107	System.err.println("Chain code " + chainCode + " not found in file " + file.getAbsolutePath());
108	System.exit(1);
109	} catch(PdbfileFormatError e) {
110	System.err.println("Formating error in file " + file.getAbsolutePath());
111	System.exit(1);
112	} catch (FileNotFoundException e) {
113	System.err.println("File " + file.getAbsolutePath() + " not found");
114	System.exit(1);
115	} catch(IOException e) {
116	System.err.println("Error reading from file " + file.getAbsolutePath());
117	System.exit(1);
118	}
119	}
120	}
121	in.close();
122
123	} catch(FileNotFoundException e) {
124	System.err.println("File " + listFile.getAbsolutePath() + " not found.");
125	System.exit(1);
126	} catch(IOException e) {
127	System.err.println("Error reading from file " + listFile.getAbsolutePath());
128	System.exit(1);
129	}
130
131	// create alignment
132	TreeMap<String,String> sequences = new TreeMap<String, String>();
133	TreeMap<String, Graph> templateGraphs = new TreeMap<String, Graph>();
134	sequences.put(targetFile.getAbsolutePath(), targetGraph.getSequence());
135	for(int i=0; i < models.size(); i++) {
136	sequences.put(modelFileNames.get(i), models.get(i).getSequence());
137	templateGraphs.put(modelFileNames.get(i), models.get(i));
138	}
139	Alignment al = new Alignment(sequences);
140
141	// create GraphAverager
142	GraphAverager grav = new GraphAverager(targetGraph.getSequence(), al, templateGraphs, targetFile.getAbsolutePath());
143	Graph resultGraph = grav.doAveraging(graphAveragingThreshold);
144
145	// compare prediction with target
146	PredEval eval = resultGraph.evaluatePrediction(targetGraph);
147	eval.print();
148
149	// write result graph to file
150	try {
151	resultGraph.write_graph_to_file("predictedGraph.cm");
152	} catch (IOException e) {
153	// TODO Auto-generated catch block
154	e.printStackTrace();
155	}
156
157	}
158	}