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NCBI C++ ToolKit: src/algo/blast/proteinkmer/unit_test/proteinkmer_unit_test.cpp Source File

kNumHits = 6;

subjid[kNumHits] = { 129296, 385145541, 448824824, 510032768, 129295, 677974076};

scores[kNumHits] = {0.359375, 0.710938, 0.242188, 0.234375, 0.28125, 0.234375};

(

index=0; index<kNumHits; index++)

pair<uint32_t, double> retval(index, scores[index]);

prelim_vector.push_back(retval);

(TSeqLocVector::iterator iter=tsl.begin(); iter != tsl.end(); ++iter)

BOOST_REQUIRE_EQUAL((*iter).seqloc->GetId()->GetGi(), subjid[index]);

(TBlastKmerScoreVector::const_iterator iter=kmerscores.begin(); iter != kmerscores.end(); ++iter)

BOOST_REQUIRE_EQUAL(sid->

(), subjid[index]);

BOOST_REQUIRE_EQUAL((*iter).second, scores[index]);

kNumQueries = 2;

kNumHits1 = 6;

kNumHits2 = 2;

subjid1[kNumHits1] = { 129296, 385145541, 448824824, 510032768, 129295, 677974076};

subjid2[kNumHits2] = { 129295, 677974076};

scores1[kNumHits1] = {0.359375, 0.710938, 0.242188, 0.234375, 0.28125, 0.234375};

scores2[kNumHits1] = {0.359375, 0.710938};

(

index=0; index<kNumHits1; index++)

pair<uint32_t, double> retval(index, scores1[index]);

prelim_vector1.push_back(retval);

(

index=0; index<kNumHits2; index++)

pair<uint32_t, double> retval(index+4, scores2[index]);

prelim_vector2.push_back(retval);

vec_set.push_back(prelim_vector1);

vec_set.push_back(prelim_vector2);

id_vec.push_back(qid1);

id_vec.push_back(qid2);

stats_vec.push_back(stats1);

stats_vec.push_back(stats2);

errs.resize(kNumQueries);

BOOST_REQUIRE_EQUAL(result_set.

(), kNumQueries);

(TBlastKmerScoreVector::const_iterator iter=kmerscores.begin(); iter != kmerscores.end(); ++iter)

BOOST_REQUIRE_EQUAL(sid->

(), subjid1[index]);

BOOST_REQUIRE_EQUAL((*iter).second, scores1[index]);

(TBlastKmerScoreVector::const_iterator iter=kmerscores2.begin(); iter != kmerscores2.end(); ++iter)

BOOST_REQUIRE_EQUAL(sid->

(), subjid2[index]);

BOOST_REQUIRE_EQUAL((*iter).second, scores2[index]);

BOOST_REQUIRE(resultsNotNULL.

() ==

);

BOOST_REQUIRE(resultsNull.

() ==

);

kNumQueries = 2;

kNumHits1 = 6;

kNumHits2 = 2;

subjid1[kNumHits1] = { 129296, 385145541, 448824824, 510032768, 129295, 677974076};

subjid2[kNumHits2] = { 129295, 677974076};

scores1[kNumHits1] = {0.359375, 0.710938, 0.242188, 0.234375, 0.28125, 0.234375};

scores2[kNumHits1] = {0.359375, 0.710938};

(

index=0; index<kNumHits1; index++)

pair<uint32_t, double> retval(index, scores1[index]);

prelim_vector1.push_back(retval);

(

index=0; index<kNumHits2; index++)

pair<uint32_t, double> retval(index+4, scores2[index]);

prelim_vector2.push_back(retval);

BOOST_REQUIRE_EQUAL(result_set.

(), kNumQueries);

(TBlastKmerScoreVector::const_iterator iter=kmerscores.begin(); iter != kmerscores.end(); ++iter)

BOOST_REQUIRE_EQUAL(sid->

(), subjid1[index]);

BOOST_REQUIRE_EQUAL((*iter).second, scores1[index]);

(TBlastKmerScoreVector::const_iterator iter=kmerscores2.begin(); iter != kmerscores2.end(); ++iter)

BOOST_REQUIRE_EQUAL(sid->

(), subjid2[index]);

BOOST_REQUIRE_EQUAL((*iter).second, scores2[index]);

(

=0;

<numHashes;

++)

(

[

] == 0);

queryseq_eaa =

;

queryseq_stdaa;

kNumHashes=128;

kKmerNum=5;

kAlphabet=0;

vector < vector <uint32_t> > seq_hash;

BOOST_REQUIRE_EQUAL(seq_hash.size(), 2);

BOOST_REQUIRE_EQUAL(seq_hash[0].

(), kNumHashes);

BOOST_REQUIRE_EQUAL(seq_hash[0][0], 529895);

BOOST_REQUIRE_EQUAL(seq_hash[0][1], 798115);

BOOST_REQUIRE_EQUAL(seq_hash[0][63], 90979);

BOOST_REQUIRE_EQUAL(seq_hash[0][83], 336201);

lsh_hash_length = 13;

lsh_hash_vals[lsh_hash_length] = { 973119,1097197,1157729,1681152,1913970,1933659,2018075,2123893,2355301,2800673,2940688,2941967,3535701};

kRowsPerBand=2;

kNumBands = kNumHashes/kRowsPerBand;

vector< vector <uint32_t> > lsh_hash_vec;

numChunks = lsh_hash_vec.size();

(

=0;

<numChunks && index<lsh_hash_length;

++)

(vector<uint32_t>::iterator iter=lsh_hash_vec[

].begin(); iter != lsh_hash_vec[

].end(); ++iter)

BOOST_REQUIRE_EQUAL(*iter, lsh_hash_vals[index]);

(index == lsh_hash_length)

queryseq_eaa =

;

queryseq_stdaa;

kNumHashes=32;

kKmerNum=5;

kAlphabet=0;

vector < vector <uint32_t> > seq_hash;

BOOST_REQUIRE_EQUAL(seq_hash.size(), 2);

BOOST_REQUIRE_EQUAL(seq_hash[0].

(), kNumHashes);

BOOST_REQUIRE_EQUAL(seq_hash[0][0], 2683052);

BOOST_REQUIRE_EQUAL(seq_hash[0][1], 26519505);

BOOST_REQUIRE_EQUAL(seq_hash[0][2], 45619224);

BOOST_REQUIRE_EQUAL(seq_hash[0][15], 396863844);

BOOST_REQUIRE(seq_hash[1][0] < seq_hash[0][1]);

BOOST_REQUIRE(seq_hash[1][1] < seq_hash[0][2]);

BOOST_REQUIRE(seq_hash[1][3] < seq_hash[0][kNumHashes-1]);

lsh_hash_length = 13;

lsh_hash_vals[lsh_hash_length] = { 700168,1293774,1377419,1712432,1819660,2314660,2484152,2944352,2951476,3273866,3625878,3709806,3837843};

kRowsPerBand=2;

vector< vector <uint32_t> > lsh_hash_vec;

numChunks = lsh_hash_vec.size();

(

=0;

<numChunks && index<lsh_hash_length;

++)

(vector<uint32_t>::iterator iter=lsh_hash_vec[

].begin(); iter != lsh_hash_vec[

].end(); ++iter)

BOOST_REQUIRE_EQUAL(*iter, lsh_hash_vals[index]);

(index == lsh_hash_length)

(

index=0; index<lshSize; index++)

kHashFct=32;

kKmerSize=5;

index_name(

);

build_index.

();

BOOST_REQUIRE_EQUAL(kKmerSize, mhfile.

());

BOOST_REQUIRE_EQUAL(0x1000001, lsh_size);

BOOST_REQUIRE_EQUAL(187, lsh_counts);

kHashFct=32;

kKmerSize=5;

index_name(

);

build_index.

();

BOOST_REQUIRE_EQUAL(kKmerSize, mhfile.

());

BOOST_REQUIRE_EQUAL(0x1000001, lsh_size);

BOOST_REQUIRE_EQUAL(213, lsh_counts);

kHashFct=32;

kKmerSize=5;

index_name(

);

build_index.

();

kHashFct=32;

kKmerSize=4;

index_name(

);

build_index.

();

BOOST_REQUIRE_EQUAL(kKmerSize, mhfile.

());

BOOST_REQUIRE_EQUAL(0x1000001, lsh_size);

BOOST_REQUIRE_EQUAL(172, lsh_counts);

kHashFct=64;

kKmerSize=4;

index_name(

);

build_index.

();

BOOST_REQUIRE_EQUAL(kKmerSize, mhfile.

());

BOOST_REQUIRE_EQUAL(0x1000001, lsh_size);

BOOST_REQUIRE_EQUAL(339, lsh_counts);

kHashFct=32;

kKmerSize=5;

kAlphabet=1;

index_name(

);

build_index.

();

BOOST_REQUIRE_EQUAL(kKmerSize, mhfile.

());

BOOST_REQUIRE_EQUAL(kAlphabet, mhfile.

());

BOOST_REQUIRE_EQUAL(0x1000001, lsh_size);

BOOST_REQUIRE_EQUAL(173, lsh_counts);

kHashFct=32;

kKmerSize=5;

kSamples=30;

kAlphabet=1;

kLSHStart=312;

index_name(

);

build_index.

();

BOOST_REQUIRE_EQUAL(kKmerSize, mhfile.

());

BOOST_REQUIRE_EQUAL(kAlphabet, mhfile.

());

BOOST_REQUIRE_EQUAL(kLSHStart, mhfile.

());

BOOST_REQUIRE_EQUAL(0x1000001, lsh_size);

BOOST_REQUIRE_EQUAL(563, lsh_counts);

BOOST_REQUIRE_EQUAL(150, chunkSize);

index_name=

;

unique_ptr<SSeqLoc> ssl(

(*loc, *scope));

query_vector.push_back(*ssl);

kmersearch(query_vector, options, seqdb);

BOOST_REQUIRE_EQUAL(opts->

(), myThresh);

BOOST_REQUIRE_EQUAL(opts->

(), hits);

BOOST_REQUIRE_EQUAL(opts->

(),

);

BOOST_REQUIRE_EQUAL(opts->

(),

);

BOOST_REQUIRE_EQUAL(opts->

(),

);

BOOST_REQUIRE_EQUAL(opts->

(),

);

unique_ptr<SSeqLoc> ssl(

(*loc, *scope));

query_vector.push_back(*ssl);

Declares the CBlastAdvancedProteinOptionsHandle class.

Interface for converting sources of sequence data into blast sequence input.

Declares the CBlastProteinOptionsHandle class.

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

vector< pair< CRef< CSeq_id >, double > > TBlastKmerScoreVector

Vector of pairs of seq-ids and scores.

vector< pair< uint32_t, double > > TBlastKmerPrelimScoreVector

Vector of pairs of database OIDs and scores.

void get_LSH_hashes(vector< vector< uint32_t > > &query_hash, vector< vector< uint32_t > > &lsh_hash_vec, int num_bands, int rows_per_band)

void get_LSH_hashes5(vector< vector< uint32_t > > &query_hash, vector< vector< uint32_t > > &lsh_hash_vec, int numHashes, int numRows)

Gets the LSH hash for one hash function.

bool minhash_query2(const string &query, vector< vector< uint32_t > > &seq_hash, int kmerNum, int numHashes, int alphabetChoice, vector< int > badMers, int chunkSize)

Hash the query for the minimum values;.

bool minhash_query(const string &query, vector< vector< uint32_t > > &seq_hash, int num_hashes, uint32_t *a, uint32_t *b, int do_seg, int kmerNum, int alphabetChoice, int chunkSize)

void Build(int numThreads=1)

Build the index.

Class of optiosn for the KMEr search.

void SetNumTargetSeqs(int matches)

Sets the number of matches (subject sequences) to return.

void SetThresh(double thresh)

Set the threshold.

void SetMinHits(int minhits)

Set the minimum number of LSH hits to initiate a calculation of the Jaccard distance.

int GetNumTargetSeqs() const

Gets the number of matches (subject sequences) to return.

double GetThresh() const

Get the threshold.

int GetMinHits() const

Get the number of LSH hits to initiate the calculation of the Jaccard distance.

bool Validate() const

Checks that options are valid.

This class holds one or more CBlastKmerResults.

size_t GetNumQueries() const

Returns the number of queries.

vector< BlastKmerStats > TBlastKmerStatsVector

Vector of KmerStats.

void push_back(value_type &element)

Add an element to m_Results.

vector< CConstRef< objects::CSeq_id > > TQueryIdVector

List of query ids.

vector< TBlastKmerPrelimScoreVector > TBlastKmerPrelimScoreVectorSet

Vector of TBlastKmerScoreVector (scores)

This class represents the results for one KMER search (one query).

Class to perform a KMER-BLASTP search.

CRef< CBlastKmerResultsSet > Run()

Performs search on one or more queries Performs search on one or more queries.

Access data in Minhash files.

int GetLSHSize(void) const

int GetNumHashes(void) const

Returns the number of values in an array of hashes (probably 32)

uint64_t * GetLSHArray(void) const

int GetVersion(void) const

int GetDataWidth(void) const

int GetChunkSize(void) const

Get number of letters in a chunk (version 3 or higher)

int GetKmerSize(void) const

Returns the length of the KMER.

int GetAlphabet(void) const

One of two alphabets from Shiryev et al.

int GetLSHStart(void) const

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

static CRef< CScope > NewScope(bool with_defaults=true)

Return a new scope, possibly (by default) with default loaders, which will include the Genbank loader...

Class for the messages for an individual query sequence.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

static void Add(const string &path)

Add the name of a dir entry; it will be deleted on (normal) exit.

@ eSerial_AsnText

ASN.1 text.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

TValue GetRand(void)

Get the next random number in the interval [0..GetMax()] (inclusive)

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

TGi GetGi(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

BOOST_AUTO_TEST_CASE(KmerResults)

void s_GetRandomNumbers(uint32_t *a, uint32_t *b, int numHashes)

int s_GetNumLSHHits(uint64_t *lsh, int lshSize)

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure for ancillary data on KMER search.

int jd_count

How often was the Jaccard distance calculated.

int hit_count

How many hits to the hash array were there?

Structure to represent a single sequence to be fed to BLAST.

Utility stuff for more convenient using of Boost.Test library.

Uniform BLAST Search Interface.

static const char * kWidth

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