1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
|
package tax;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map.Entry;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Parse;
import shared.Timer;
import shared.Tools;
public class ImgRecord implements Serializable {
private static final long serialVersionUID = 6438551103300423985L;
public static void main(String[] args){
String in=args[0];
String out=args.length>1 ? args[1] : null;
if(!Tools.testInputFiles(false, true, in)){
throw new RuntimeException("\nCan't read some input files.\n");
}
if(!Tools.testOutputFiles(true, false, false, out)){
throw new RuntimeException("\nCan't write to some output files.\n");
}
Timer t=new Timer();
HashMap<Long, ImgRecord> map=toMap(in, TaxTree.IMG_HQ);
t.stop();
System.err.println(map.size()+"; "+t);
// if(out!=null){ReadWrite.writeObjectInThread(map, out, false);}
if(out!=null){writeAsText(map, out);}
}
private static void writeAsText(HashMap<Long, ImgRecord> map, String out){
TextStreamWriter tsw=new TextStreamWriter(out, true, false, false);
for(Entry<Long, ImgRecord> e : map.entrySet()){
tsw.println(e.toString());
}
}
@Override
public String toString(){
StringBuilder sb=new StringBuilder();
sb.append(imgID);
sb.append('\t').append(taxID);
sb.append('\t').append(name);
return sb.toString();
}
public static HashMap<Long, ImgRecord> toMap(String fname, boolean highQuality){
ImgRecord[] array=toArray(fname, highQuality);
HashMap<Long, ImgRecord> map=new HashMap<Long, ImgRecord>((3+array.length*4)/3);
for(ImgRecord ir : array){
map.put(ir.imgID, ir);
}
return map;
}
public static ImgRecord[] toArray(String fname, boolean highQuality){
TextFile tf=new TextFile(fname, false);
ArrayList<ImgRecord> list=new ArrayList<ImgRecord>();
for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
if(line.length()<1 || !Tools.isDigit(line.charAt(0))){
//do nothing
}else{
ImgRecord record=new ImgRecord(line);
if(!highQuality || record.highQuality){list.add(record);}
}
}
tf.close();
return list.toArray(new ImgRecord[0]);
}
public ImgRecord(String line){
String[] split=line.split("\t");
imgID=Long.parseLong(split[0]);
name=(storeName ? split[1] : null);
try {
taxID=(split[2]==null || split[2].length()<1 ? -1 : Integer.parseInt(split[2]));
} catch (NumberFormatException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
System.err.println(line);
throw new RuntimeException();
}
isPublic=Parse.parseYesNo(split[3]);
obsolete=Parse.parseYesNo(split[4]);
genomeType=find(split[5], typeArray);
boolean hq=false;
if(split.length>7){
try {
hq=Parse.parseYesNo(split[7]);
} catch (Exception e) {
System.err.println(Arrays.toString(split));
assert(false);
}
}
highQuality=hq;
}
public final long imgID;
public final int taxID;
public final int genomeType;
public final boolean isPublic;
public final boolean obsolete;
public final boolean highQuality;
public final String name;
public final String path(){return "/global/dna/projectdirs/microbial/img_web_data/taxon.fna/"+imgID+".fna";}
final int ISOLATE=0, SINGLE_CELL=1, METAGENOME=2;
final String[] typeArray={"isolate", "single_cell", "metagenome"};
private static int find(String s, String[] array){
for(int i=0; i<array.length; i++){
if(array[i].equals(s)){return i;}
}
return -1;
}
public static boolean storeName=true;
public static HashMap<Long, ImgRecord> imgMap;
// public static final String DefaultDumpFile="/global/cfs/cdirs/bbtools/tax/imgTaxDump.txt.gz";
public static final String DefaultDumpFile="/global/u1/i/img/adhocDumps/taxonDumpForBrian.txt";
}
|
