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View Code? Open in Web Editor NEWFull length circRNA reconstruction and quantification using BSJ and reverse overlap (RO) features.
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师兄师姐你们好，想了解一下circAtlas的问题。
您好，看到这几天circAtlas在数据更新，想请教您数据库中 full length 和 mature length的情况。
我发现有接近1/3的circRNA都存在【human_bed_v2.0.txt】提供的全长坐标，和【human_sequence_v2.0.txt】 文件中circRNA 两端的序列对不上，如下图所示。
我看了CIRI-as和CIRI-full的算法，还有其他4个circRNA的鉴定软件，都有基于1-3形成BSJ位点来鉴定。那为什么mature length 的BSJ位点又变成了 1-2（这种情况在很多4个软件同时鉴定到的circRNA中也有）
祝好！
算法请教
您好!
请教一下您这一步数据分类的具体数据清洗是怎样的一个逻辑!
while (line.substring(0, 1).equals("@") == true) {
String[] tmphead = line.split(" ");
if (tmphead[0].equals("@SQ")) {
String[] tmphead1 = tmphead[1].split("\\:");
String[] tmphead2 = tmphead[2].split("\\:");
// System.out.println(tmphead1[1]);
if (Integer.parseInt(tmphead2[1]) > 500000)
name.add(tmphead1[1]);
}
line = reader.readLine();
///part the file with chr;
}
File[] tmpfile = new File[name.size()];
int mat = 0;
while (mat < name.size()) {
tmpfile[mat] = File.createTempFile("tmp" + name.get(mat) + "_", ".txt", f);
tmpfile[mat].deleteOnExit();
// System.out.println(tmpfile[mat]);
map.put(name.get(mat), tmpfile[mat]);
mat++;
}
int onepart = 200000;
int linenum = 0;
ArrayList<String> text = new ArrayList<String>();
while (line != null) {
String[] tmpt = line.split(" ");
if (!tmpt[2].equals("*")) {
text.add(line);
linenum++;
} else
num5++;
if (linenum > onepart) {
String A = line;
line = reader.readLine();
String[] tmpt2 = line.split(" ");
while (tmpt[0].equals(tmpt2[0])) {
text.add(line);
A = line;
line = reader.readLine();
tmpt = A.split(" ");
tmpt2 = line.split(" ");
}
String[] G1 = new String[10000];
String[] tmp1;
mat = 0;
while (mat < name.size()) {
FileOutputStream out = new FileOutputStream(tmpfile[mat], true);
PrintStream p1 = new PrintStream(out);
int k = 1;
int n = 0;
while (k - 1 < text.size()) {
int p;
tmp1 = text.get(k - 1).split(" ");
if (k >= text.size())
p = 1;
else {
String[] tmp2 = text.get(k).split(" ");
if (tmp1[0].equals(tmp2[0]) == true)
p = 0;
else
p = 1;
}
if (p == 0) {
G1[n] = text.get(k - 1);
n++;
} else {
G1[n] = text.get(k - 1);
String[] tmp = G1[0].split(" ");
// System.out.println(map.get(tmpfile[mat]));
if (tmp[2].equals(name.get(mat))) {
int nn = 0;
while (nn <= n) {
p1.println(G1[nn]);
nn++;
}
}
n = 0;
}
k++;
}
p1.close();
mat++;
}
text = new ArrayList<String>();
linenum = 0;
System.out.print(".");
} else {
line = reader.readLine();
}
}
if (linenum > 0) {
String[] G1 = new String[10000];
String[] tmp1;
mat = 0;
while (mat < name.size()) {
FileOutputStream out = new FileOutputStream(tmpfile[mat], true);
PrintStream p1 = new PrintStream(out);
int k = 1;
int n = 0;
while (k - 1 < text.size()) {
int p;
tmp1 = text.get(k - 1).split(" ");
if (k >= text.size())
p = 1;
else {
String[] tmp2 = text.get(k).split(" ");
if (tmp1[0].equals(tmp2[0]) == true)
p = 0;
else
p = 1;
}
if (p == 0) {
G1[n] = text.get(k - 1);
n++;
} else {
G1[n] = text.get(k - 1);
String[] tmp = G1[0].split(" ");
// System.out.println(map.get(tmpfile[mat]));
if (tmp[2].equals(name.get(mat))) {
int nn = 0;
while (nn <= n) {
p1.println(G1[nn]);
nn++;
}
}
n = 0;
}
k++;
}
p1.close();
mat++;
}
text = new ArrayList<String>();
linenum = 0;
System.out.print(".");
}
reader.close();
System.out.println("Apart completed");
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