我是D的新手,想要解析形式的生物文件
>name1
acgcgcagagatatagctagatcg
aagctctgctcgcgct
>name2
acgggggcttgctagctcgatagatcga
agctctctttctccttcttcttctagagaga
>name2
gag ggagag
这样我就可以使用相应的'序列'数据捕获'header'name1,name2,name3,..acgcg ...... stuff。
现在我有了这个。但它只会逐行迭代,
import std.stdio;
import std.stream;
import std.regex;
int main(string[] args){
auto filename = args[1];
auto entry_name = regex(r"^>(.*)"); //captures header only
auto fasta_regex = regex(r"(\>.+\n)([^\>]+\n)"); //captures header and correponding sequence
try {
Stream file = new BufferedFile(filename);
foreach(ulong n, char[] line; file) {
auto name_capture = match(line,entry_name);
writeln(name_capture.captures[1]);
}
file.close();
}
catch (FileException xy){
writefln("Error reading the file: ");
}
catch (Exception xx){
writefln("Exception occured: " ~ xx.toString());
}
return 0;
}
我想知道一种提取标题和序列数据的好方法,这样我就可以创建一个关联数组,其中每个项目对应于文件中的一个条目
[name1:acgcgcagagatatagctagatcgaagctctgctcgcgct,name2:acgggggcttgctagctcgatagatcgaagctctctttctccttcttcttctagagaga,.....]
答案 0 :(得分:8)
标题在它自己的行上吗?所以为什么不检查它并使用appender来分配值
auto current = std.array.appender!(char[]);
string name;
foreach(ulong n, char[] line; file) {
auto entry = match(line,entry_name);
if(entry){//we are in a header line
if(name){//write what was caught
map[name]=current.data.dup;//dup because .current.data is reused
}
name = entry.hit.idup;
current.clear();
}else{
current.put(line);
}
}
map[name]=current.data.dup;//remember last capture
地图是您存储值的地方(string[string]
将会这样做)
答案 1 :(得分:5)
这是我没有正则表达式的解决方案(我不相信这么简单的输入我们需要regexp):
import std.stdio;
import std.stream;
int main(string[] args) {
int ret = 0;
string fileName = args[1];
string header;
char[] sequence;
string[string] content;
try {
auto file = new BufferedFile(fileName);
foreach(ulong lineNumber, char[] line; file) {
if (line[0] == '>') {
if (header.length > 0) {
content[header] = sequence.idup;
sequence.length = 0;
} // if
// we have a new header, and new sequence will start after it
header = line[1..$].idup;
content[header] = "";
} else {
sequence ~= line;
} // else
} // foreach
content[header] = sequence.idup;
file.close();
}
catch (OpenException oe){
writefln("Error opening file: " ~ oe.toString());
}
catch (Exception e){
writefln("Exception: " ~ e.toString());
}
writeln(content);
return ret;
} // main() function
/+ -------------------------- BEGIN OUTPUT ------------------------------- +
["name3":"gag ggagag", "name1":"acgcgcagagatatagctagatcgaagctctgctcgcgct", "name2":"acgggggcttgctagctcgatagatcgaagctctctttctccttcttcttctagagaga"]
+ -------------------------- END OUTPUT --------------------------------- +/