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
|
#include <iostream>
#include <seqan/sequence.h>
#include <seqan/stream.h>
#include <seqan/store.h>
using namespace seqan2;
int main()
{
CharString fileName = getAbsolutePath("demos/tutorial/genome_annotations/assignment_annotations.gtf");
GffFileIn file(toCString(fileName));
FragmentStore<> store;
readRecords(store, file);
// Create iterator
Iterator<FragmentStore<>, AnnotationTree<> >::Type it;
it = begin(store, AnnotationTree<>());
// Iterate to the first annotation of type "exon"
while (!atEnd(it) && getType(it) != "exon")
goNext(it);
// Output:
std::cout << " type: " << getType(it) << std::endl;
std::cout << " begin position: " << getAnnotation(it).beginPos << std::endl;
std::cout << " end position: " << getAnnotation(it).endPos << std::endl;
std::cout << " id: " << value(it) << std::endl;
std::cout << " parent id: " << getAnnotation(it).parentId << std::endl;
std::cout << " parent name: " << getParentName(it) << std::endl;
return 0;
}
|
