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
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
|
package prok;
import java.util.ArrayList;
import fileIO.ByteFile;
import shared.Parse;
import shared.Tools;
public class GeneModelParser {
GeneModelParser(String fname_){
fname=fname_;
lines=ByteFile.toLines(fname);
gm=new GeneModel(false);
}
boolean hasMore(){
return pos<lines.size();
}
byte[] nextLine(){
if(pos>=lines.size()){return null;}
byte[] line=lines.get(pos);
pos++;
return line;
}
final String fname;
final ArrayList<byte[]> lines;
private final GeneModel gm;
int pos=0;
/*--------------------------------------------------------------*/
/*---------------- Parsing ----------------*/
/*--------------------------------------------------------------*/
public static GeneModel loadModel(String fname) {
GeneModelParser gmp=new GeneModelParser(fname);
return gmp.parse();
}
private GeneModel parse(){
while(hasMore()){
byte[] line=nextLine();
boolean valid=parseHeader(line);
if(!valid){
pos--;
break;
}
}//Done parsing headers
ArrayList<StatsContainer> containers=new ArrayList<StatsContainer>();
while(hasMore()){
StatsContainer sc=parseContainer();
if(sc!=null){
containers.add(sc);
}else{
assert(false);
}
}
assert(containers.size()==6) : containers.size();
for(StatsContainer sc : containers){
gm.allContainers[sc.type].setFrom(sc);
}
// gm.statsCDS.setFrom(containers.get(0);
// gm.statstRNA=containers.get(1);
// gm.stats16S=containers.get(2);
// gm.stats23S=containers.get(3);
// gm.stats5S=containers.get(4);
// gm.stats18S=containers.get(5);
// gm.stats16S.minIdentity=ProkObject.min16SIdentity;
// gm.stats23S.minIdentity=ProkObject.min23SIdentity;
// gm.stats18S.minIdentity=ProkObject.min18SIdentity;
gm.setStatics();
return gm;
}
private StatsContainer parseContainer(){
String name=null;
int type=-1;
long lengthCount=0;
long lengthSum=0;
for(byte[] line=nextLine(); line!=null; line=nextLine()){
if(line[0]!='#'){
pos--;
break;
}
if(Tools.startsWith(line, "##")){
//ignore
}else if(Tools.startsWith(line, "#name")){
name=parseString(line);
}else if(Tools.startsWith(line, "#type")){
type=parseInt(line);
}else if(Tools.startsWith(line, "#count")){
lengthCount=parseLong(line);
}else if(Tools.startsWith(line, "#lengthSum")){
lengthSum=parseLong(line);
}else if(Tools.startsWith(line, "#contains")){
break;
}else{
assert(false) : new String(line);
}
}
ArrayList<FrameStats> list=new ArrayList<FrameStats>(3);
for(int i=0; i<3; i++){
FrameStats fs=parseStats();
list.add(fs);
}
StatsContainer sc=new StatsContainer(type);
assert(sc.name.equals(name)) : name+", "+sc.name+", "+type;
sc.lengthCount=lengthCount;
sc.lengthSum=lengthSum;
sc.setInner(list.get(0));
sc.setStart(list.get(1));
sc.setStop(list.get(2));
sc.calculate();
assert(sc.inner!=null);
return sc;
}
private FrameStats parseStats(){
String name=null;
int k=-1, frames=-1, offset=-1;
// System.err.println("A");
for(byte[] line=nextLine(); line!=null; line=nextLine()){
if(line[0]!='#'){
pos--;
// System.err.println("B");
assert(false) : new String(line);
break;
}
if(Tools.startsWith(line, "##")){
//ignore
}else if(Tools.startsWith(line, "#name")){
name=parseString(line);
}else if(Tools.startsWith(line, "#k")){
k=parseInt(line);
}else if(Tools.startsWith(line, "#frames")){
frames=parseInt(line);
}else if(Tools.startsWith(line, "#offset")){
offset=parseInt(line);
}else if(Tools.startsWith(line, "#valid\tframe")){
// assert(false);
// System.err.println("C");
break;
}
// System.err.println("D");
}
// assert(false);
// System.err.println("E");
FrameStats fs=new FrameStats(name, k, frames, offset);
for(int i=0, max=2*fs.frames; i<max; i++){
byte[] line=nextLine();
fs.parseData(line);
}
return fs;
}
private static String parseString(byte[] line){
int idx=Tools.indexOf(line, '\t');
String s=new String(line, idx+1, line.length-idx-1);
return s;
}
private static int parseInt(byte[] line){
int idx=Tools.indexOf(line, '\t');
return Parse.parseInt(line, idx+1, line.length);
}
private static long parseLong(byte[] line){
int idx=Tools.indexOf(line, '\t');
return Parse.parseLong(line, idx+1, line.length);
}
// public static void parseHeaderStatic(byte[] line){
//
// assert(line[0]=='#');
// if(Tools.startsWith(line, "#k_inner")){
// int x=(int)parseLong(line);
// assert(x==innerKmerLength);
// setInnerK(x);
// }else if(Tools.startsWith(line, "#k_end")){
// int x=(int)parseLong(line);
// assert(x==endKmerLength);
// setEndK(x);
// }else if(Tools.startsWith(line, "#start_left_offset")){
// int x=(int)parseLong(line);
// assert(x==startLeftOffset);
// setStartLeftOffset(x);
// }else if(Tools.startsWith(line, "#start_right_offset")){
// int x=(int)parseLong(line);
// assert(x==startRightOffset);
// setStartRightOffset(x);
// }else if(Tools.startsWith(line, "#stop_left_offset")){
// int x=(int)parseLong(line);
// assert(x==stopLeftOffset);
// setStopLeftOffset(x);
// }else if(Tools.startsWith(line, "#stop_right_offset")){
// int x=(int)parseLong(line);
// assert(x==stopRightOffset);
// setStopRightOffset(x);
// }
// }
public boolean parseHeader(byte[] line){
if(line[0]!='#'){return false;}
if(Tools.startsWith(line, "#BBMap")){
//ignore
}else if(Tools.startsWith(line, "##")){
//ignore
}else if(Tools.startsWith(line, "#files")){//Not necessary
String[] split=new String(line).split("\t");
try {
gm.numFiles+=Integer.parseInt(split[1]);
} catch (NumberFormatException e) {
gm.numFiles+=split.length-1;//old style pgm
}
// for(String s : new String(line).split("\t")){
// if(s.charAt(0)!='#'){
// gm.fnames.add(s);
// }
// }
}else if(Tools.startsWith(line, "#taxIDs")){//Can be made faster
for(String s : new String(line).split("\t")){
if(s.charAt(0)!='#'){
gm.taxIds.add(Integer.parseInt(s));
}
}
}else if(Tools.startsWith(line, "#scaffolds")){
long x=parseLong(line);
gm.readsProcessed=x;
}else if(Tools.startsWith(line, "#bases")){
long x=parseLong(line);
gm.basesProcessed=x;
}else if(Tools.startsWith(line, "#genes")){
long x=parseLong(line);
gm.genesProcessed=x;
}else if(Tools.startsWith(line, "#GC")){
//ignore
}else if(Tools.startsWith(line, "#ACGTN")){
String[] split=new String(line).split("\t");
for(int i=0; i<gm.baseCounts.length; i++){
gm.baseCounts[i]=Long.parseLong(split[i+1]);
}
}else{
return false;
}
return true;
}
}
|
