| Example Program Blast Reports Parsing the output of BLAST call. A tutorial about parsing a blast report.
1 | #include <iostream>
| 2 | #include <seqan/blast.h>
| 3 |
| 4 | using namespace seqan;
| 5 |
| 6 |
| 7 | template <typename TFile>
| 8 | void read_blast_report(TFile & strm)
| 9 | {
| 10 |
|
11 | typedef BlastHsp<BlastN, FullInfo> TBlastHsp;
| 12 |
|
13 | typedef BlastReport<TBlastHsp, StreamReport<TFile> > TBlastReport;
| 14 | typedef typename Hit<TBlastReport>::Type TBlastHit;
| 15 | typedef typename Iterator<TBlastReport,HitIterator>::Type THitIterator;
| 16 | typedef typename Iterator<TBlastHit,HspIterator>::Type THspIterator;
| 17 |
| 18 |
|
21 | unsigned hspcount = 0;
| 22 | unsigned hitcount = 0;
| 23 | unsigned highsignif = 0;
| 24 |
| 25 | while(!atEnd(strm,blast))
| 26 | {
|
27 | read(strm,blast,Blast());
| 28 | ::std::cout << "Query: "<<getQueryName(blast) <<"\n";
| 29 | ::std::cout << "Database: "<<getDatabaseName(blast) <<"\n\n";
| 30 |
|
31 | THitIterator hit_it(blast);
| 32 | for(; !atEnd(strm,hit_it); goNext(strm,hit_it))
| 33 | {
| 34 | ++hitcount;
| 35 | TBlastHit hit = getValue(strm,hit_it);
| 36 | ::std::cout << " Hit: " <<name(hit) <<"\n\n";
| 37 |
| 38 | /// iterate over alignments (HSPs)
| 39 | THspIterator hsp_it(hit);
| 40 | for(; !atEnd(strm,hsp_it); goNext(strm,hsp_it))
| 41 | {
| 42 | ++hspcount;
| 43 | TBlastHsp hsp = getValue(strm,hsp_it);
| 44 |
|
45 | ::std::cout << " Score = " << getBitScore(hsp) << "\n";
| 46 | ::std::cout << " Length = " << length(hsp) << "\n\n";
|
47 | if(getEValue(hsp)<0.01)
| 48 | ++highsignif;
| 49 |
| 50 | }
| 51 | }
| 52 | }
| 53 | ::std::cout <<"Total number of Hits: "<< hitcount<<::std::endl;
| 54 | ::std::cout <<"Total number of HSPs: "<< hspcount<<::std::endl;
| 55 | ::std::cout <<"Number of highly significant HSPs: "<< highsignif<<::std::endl;
| 56 |
| 57 | }
| 58 |
| 59 |
| 60 | int main()
| 61 | {
| 62 | ::std::fstream strm;
| 63 | strm.open("ecoln.out", ::std::ios_base::in | ::std::ios_base::binary);
| 64 | read_blast_report(strm);
| 65 | return 0;
| 66 | }
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