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English alphabet #6

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1573f1b
Added script to build library
jeevannavar Oct 18, 2021
8baae8f
Added English alphabet for search
jeevannavar Oct 18, 2021
8549f25
Added english alphabet arguments and calls
jeevannavar Oct 18, 2021
477a0e9
Corrected errors
jeevannavar Oct 19, 2021
799791d
Added all requisite support for English alphabet
jeevannavar Oct 19, 2021
f34f1db
modifications
jeevannavar Dec 1, 2022
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9 changes: 9 additions & 0 deletions build.sh
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@@ -0,0 +1,9 @@
rm -rf build
mkdir build
cd build
cmake -Wno-dev ..
cmake --build . --config Release

# Additionally, either copy the nsearch file from build/nsearch to /usr/local/bin or add the directory to path
# sudo cp nsearch/nsearch /usr/local/bin/
# something like echo $PATH:$PWD/build/nsearch added to bashrc or something
19 changes: 19 additions & 0 deletions libnsearch/include/nsearch/Alnout/Writer.h
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Expand Up @@ -4,6 +4,7 @@

#include "../Alphabet/DNA.h"
#include "../Alphabet/Protein.h"
#include "../Alphabet/English.h"

#include <fstream>

Expand Down Expand Up @@ -331,4 +332,22 @@ inline std::string Writer< Protein >::Unit() {
return "aa";
}

// English specializations
template <>
inline char Writer< English >::MatchSymbol( const char A, const char B ) {
auto score = ScorePolicy< English >::Score( A, B );
if( score >= 10 )
return '|';
if( score >= 5 )
return ':';
if( score > 0 )
return '.';
return ' ';
}

template <>
inline std::string Writer< English >::Unit() {
return "Letter";
}

} // namespace Alnout
99 changes: 99 additions & 0 deletions libnsearch/include/nsearch/Alphabet/English.h
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#pragma once

#include "../Alphabet.h"

struct English {
typedef char CharType;
};

// Scoring: First Try. Looking for exact match.
// Collapse letters into 5 bits
template <>
struct BitMapPolicy< English > {
static const size_t NumBits = 5;

inline static int8_t BitMap( const char letter ) {
static const uint8_t BitMapping[] = {
0b000000, // 'A'
0b000001, // 'B'
0b000010, // 'C'
0b000011, // 'D'
0b000100, // 'E'
0b000101, // 'F'
0b000110, // 'G'
0b000111, // 'H'
0b001000, // 'I'
0b001001, // 'J'
0b001010, // 'K'
0b001011, // 'L'
0b001100, // 'M'
0b001101, // 'N'
0b001110, // 'O'
0b001111, // 'P'
0b010000, // 'Q'
0b010001, // 'R'
0b010010, // 'S'
0b010011, // 'T'
0b010101, // 'U'
0b010110, // 'V'
0b010111, // 'W'
0b011000, // 'X'
0b011001, // 'Y'
0b011010, // 'Z'
0b011011, // ' ' space
};

auto val = BitMapping[ letter - 'A' ];
// if( ( val & 0b010000 ) > 0 )
// return -1; // ambiguity

return ( val & 0b01111 );
}
};

// BLOSUM62
template <>
struct ScorePolicy< English > {
inline static int8_t Score( const char letterA, const char letterB ) {
static const int ScoreMatrixSize = 27; // 'A'...'Z' and ' '
static const int8_t ScoreMatrix[ ScoreMatrixSize ][ ScoreMatrixSize ] = {
/* A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, */
{ 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // A
{ 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // B
{ 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // C
{ 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // D
{ 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // E
{ 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // F
{ 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // G
{ 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // H
{ 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // I
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // J
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // K
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // L
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // M
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // N
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // O
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // P
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // Q
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0}, // R
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0}, // S
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0}, // T
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0}, // U
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0}, // V
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0}, // W
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0}, // X
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0}, // Y
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0}, // Z
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1}, //
};

return ScoreMatrix[ letterA - 'A' ][ letterB - 'A' ];
}
};

template <>
struct MatchPolicy< English > {
inline static bool Match( const char letterA, const char letterB ) {
return ScorePolicy< English >::Score( letterA, letterB ) >= 4;
}
};
14 changes: 14 additions & 0 deletions libnsearch/include/nsearch/Database/GlobalSearch.h
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Expand Up @@ -140,6 +140,20 @@ void GlobalSearch< A >::SearchForHits( const Sequence< A >& query,
for( auto& sp : sps ) {
size_t queryPos, candidatePos;

// check if we already have a HSP which this SP is part of
bool isContained = false;
for( auto it = hsps.cbegin(); it != hsps.cend(); ++it ) {
const HSP& hsp = *it;
if (sp.IsFullyContainedWithin(hsp)) {
isContained = true;
break;
}
}

// do not extend this, since it's part of an HSP already
if (isContained)
continue;

size_t a1 = sp.a1, a2 = sp.a2, b1 = sp.b1, b2 = sp.b2;

Cigar leftCigar;
Expand Down
5 changes: 5 additions & 0 deletions libnsearch/include/nsearch/Database/HSP.h
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Expand Up @@ -32,6 +32,11 @@ class HSP {
return ( a1 <= other.a2 && other.a1 <= a2 ) // overlap in A direction
|| ( b1 <= other.b2 && other.b1 <= b2 ); // overlap in B direction
}
bool IsFullyContainedWithin( const HSP& other) const {
return (other.a1 <= a1 && other.a2 >= a2) &&
(other.b1 <= b1 && other.b2 >= b2);
}


size_t DistanceTo( const HSP& other ) const {
size_t dx = ( a1 > other.a2 ? a1 - other.a2 : other.a1 - a2 );
Expand Down
5 changes: 4 additions & 1 deletion nsearch/src/Main.cpp
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Expand Up @@ -8,6 +8,7 @@
#include <nsearch/Sequence.h>
#include <nsearch/Alphabet/DNA.h>
#include <nsearch/Alphabet/Protein.h>
#include <nsearch/Alphabet/English.h>

#include "Common.h"
#include "Filter.h"
Expand All @@ -22,7 +23,7 @@ static const char USAGE[] = R"(

Usage:
nsearch search --query=<queryfile> --db=<databasefile>
--out=<outputfile> --min-identity=<minidentity> [--max-hits=<maxaccepts>] [--max-rejects=<maxrejects>] [--protein] [--strand=<strand>]
--out=<outputfile> --min-identity=<minidentity> [--max-hits=<maxaccepts>] [--max-rejects=<maxrejects>] [--protein] [--english] [--strand=<strand>]
nsearch merge --forward=<forwardfile> --reverse=<reversefile> --out=<outputfile>
nsearch filter --in=<inputfile> --out=<outputfile> [--max-expected-errors=<maxee>]

Expand Down Expand Up @@ -100,6 +101,8 @@ int main( int argc, const char** argv ) {

if( args[ "--protein" ].asBool() ) {
DoSearch< Protein >( query, db, out, ParseSearchParams< Protein >( args ) );
} else if ( args[ "--english" ].asBool() ) {
DoSearch< English >( query, db, out, ParseSearchParams< English >( args ) );
} else {
DoSearch< DNA >( query, db, out, ParseSearchParams< DNA >( args ) );
}
Expand Down
9 changes: 9 additions & 0 deletions nsearch/src/Search.cpp
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Expand Up @@ -6,6 +6,7 @@
#include <nsearch/Sequence.h>
#include <nsearch/Alphabet/DNA.h>
#include <nsearch/Alphabet/Protein.h>
#include <nsearch/Alphabet/English.h>

#include <memory>

Expand Down Expand Up @@ -105,6 +106,11 @@ struct WordSize< Protein > {
static const int VALUE = 5;
};

template <>
struct WordSize< English > {
static const int VALUE = 5;
};

template < typename A >
bool DoSearch( const std::string& queryPath, const std::string& databasePath,
const std::string& outputPath,
Expand Down Expand Up @@ -202,3 +208,6 @@ template bool DoSearch< DNA >( const std::string&, const std::string&,
template bool DoSearch< Protein >( const std::string&, const std::string&,
const std::string&,
const SearchParams< Protein >& );
template bool DoSearch< English >( const std::string&, const std::string&,
const std::string&,
const SearchParams< English >& );