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#include <iostream>
#include <seqan/store.h>
#include <seqan/arg_parse.h>
#include <seqan/misc/interval_tree.h>
#include <seqan/parallel.h>
using namespace seqan2;
//![definitions]
// define used types
typedef FragmentStore<> TStore;
typedef Value<TStore::TAnnotationStore>::Type TAnnotation;
typedef TAnnotation::TId TId;
typedef TAnnotation::TPos TPos;
typedef IntervalAndCargo<TPos, TId> TInterval;
typedef IntervalTree<TPos, TId> TIntervalTree;
typedef Value<TStore::TAlignedReadStore>::Type TAlignedRead;
//![definitions]
//![definitions_end]
//
// 1. Load annotations and alignments from files
//
bool loadFiles(TStore & store, std::string const & annotationFileName, std::string const & alignmentFileName)
{
BamFileIn alignmentFile;
if (!open(alignmentFile, alignmentFileName.c_str()))
{
std::cerr << "Couldn't open alignment file " << alignmentFileName << std::endl;
return false;
}
std::cout << "Loading read alignments ..... " << std::flush;
readRecords(store, alignmentFile);
std::cout << "[" << length(store.alignedReadStore) << "]" << std::endl;
// load annotations
GffFileIn annotationFile;
if (!open(annotationFile, toCString(annotationFileName)))
{
std::cerr << "Couldn't open annotation file" << annotationFileName << std::endl;
return false;
}
std::cout << "Loading genome annotation ... " << std::flush;
readRecords(store, annotationFile);
std::cout << "[" << length(store.annotationStore) << "]" << std::endl;
return true;
}
//
// 2. Extract intervals from gene annotations (grouped by contigId)
//
void extractGeneIntervals(String<String<TInterval> > & intervals, TStore const & store)
{
// extract intervals from gene annotations (grouped by contigId)
resize(intervals, length(store.contigStore));
Iterator<TStore const, AnnotationTree<> >::Type it = begin(store, AnnotationTree<>());
if (!goDown(it))
return;
do
{
SEQAN_ASSERT_EQ(getType(it), "gene");
TPos beginPos = getAnnotation(it).beginPos;
TPos endPos = getAnnotation(it).endPos;
TId contigId = getAnnotation(it).contigId;
if (beginPos > endPos)
std::swap(beginPos, endPos);
// insert forward-strand interval of the gene and its annotation id
appendValue(intervals[contigId], TInterval(beginPos, endPos, value(it)));
}
while (goRight(it));
}
//
// 3. Construct interval trees
//
void constructIntervalTrees(String<TIntervalTree> & intervalTrees,
String<String<TInterval> > & intervals)
{
int numContigs = length(intervals);
resize(intervalTrees, numContigs);
SEQAN_OMP_PRAGMA(parallel for)
for (int i = 0; i < numContigs; ++i)
createIntervalTree(intervalTrees[i], intervals[i]);
}
//![definitions_end]
//![yourcode]
//
// 4. Count reads per gene
//
void countReadsPerGene(String<unsigned> & readsPerGene, String<TIntervalTree> const & intervalTrees, TStore const & store)
{
(void) readsPerGene;
(void) intervalTrees;
(void) store;
// INSERT YOUR CODE HERE ...
//
}
//![yourcode]
//![yourcode_end]
int main(int, char const **)
{
TStore store;
String<String<TInterval> > intervals;
//![yourcode_end]
//![main]
String<TIntervalTree> intervalTrees;
String<unsigned> readsPerGene;
//![main]
//![main_end]
std::string annotationFileName = getAbsolutePath("demos/tutorial/simple_rna_seq/example.gtf");
std::string alignmentFileName = getAbsolutePath("demos/tutorial/simple_rna_seq/example.sam");
if (!loadFiles(store, annotationFileName, alignmentFileName))
return 1;
//![main_end]
//![main2]
extractGeneIntervals(intervals, store);
constructIntervalTrees(intervalTrees, intervals);
countReadsPerGene(readsPerGene, intervalTrees, store);
//![main2]
//![main2_end]
return 0;
}
//![main2_end]
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