From 39362acf7d59124cedab0adb4ed09ecf32611af4 Mon Sep 17 00:00:00 2001 From: Dariusz Murakowski Date: Thu, 23 Apr 2015 00:27:50 -0400 Subject: [PATCH] Decipher Potts encoding of sequence state/configuration. --- Makefile | 2 +- seqTools.cpp | 146 ++++++++++++++++++++++++++++++++++++++++++++++++----------- snip.cpp | 27 +++++++++++ 3 files changed, 147 insertions(+), 28 deletions(-) diff --git a/Makefile b/Makefile index 13ad714..98b38b5 100644 --- a/Makefile +++ b/Makefile @@ -19,7 +19,7 @@ LIBS = -lgsl -lgslcblas -lm # = `gsl-config --libs` ifeq ($(dbg),1) - DBGFLAG = -g -DDEBUG + DBGFLAG = -g -DDEBUG # -D_GLIBCXX_DEBUG else DBGFLAG = -O3 -combine endif diff --git a/seqTools.cpp b/seqTools.cpp index 3a831de..44c9f0d 100644 --- a/seqTools.cpp +++ b/seqTools.cpp @@ -1,7 +1,14 @@ #include +#include +#include +#include #include -enum class aa {unknown, A,R,N,D,C, Q,E,G,H,I, L,K,M,F,P, S,T,W,Y,V, B,Z,X, star, gap,}; +typedef std::vector > IntVector; +typedef std::vector > CharVector; + +//enum class aa {BEGIN, unknown=BEGIN, A,R,N,D,C, Q,E,G,H,I, L,K,M,F,P, S,T,W,Y,V, B,Z,X, star, gap, END}; +enum aa {aa_BEGIN, aa_unknown=aa_BEGIN, aa_A,aa_R,aa_N,aa_D,aa_C, aa_Q,aa_E,aa_G,aa_H,aa_I, aa_L,aa_K,aa_M,aa_F,aa_P, aa_S,aa_T,aa_W,aa_Y,aa_V, aa_B,aa_Z,aa_X, aa_star, aa_gap, aa_END}; enum class nt {T,C,A,G}; enum class codon {TTT,TTC,TTA,TTG, TCT,TCC,TCA,TCG, TAT,TAC,TAA,TAG, TGT,TGC,TGA,TGG, CTT,CTC,CTA,CTG, CCT,CCC,CCA,CCG, CAT,CAC,CAA,CAG, CGT,CGC,CGA,CGG, @@ -31,22 +38,22 @@ namespace std { } codon2aa_map codon2aa { - {codon::TTT, aa::F}, {codon::TTC, aa::F}, {codon::TTA, aa::L}, {codon::TTG, aa::L}, - {codon::TCT, aa::S}, {codon::TCC, aa::S}, {codon::TCA, aa::S}, {codon::TCG, aa::S}, - {codon::TAT, aa::Y}, {codon::TAC, aa::Y}, {codon::TAA, aa::star}, {codon::TAG, aa::star}, - {codon::TGT, aa::C}, {codon::TGC, aa::C}, {codon::TGA, aa::star}, {codon::TGG, aa::W}, - {codon::CTT, aa::L}, {codon::CTC, aa::L}, {codon::CTA, aa::L}, {codon::CTG, aa::L}, - {codon::CCT, aa::P}, {codon::CCC, aa::P}, {codon::CCA, aa::P}, {codon::CCG, aa::P}, - {codon::CAT, aa::H}, {codon::CAC, aa::H}, {codon::CAA, aa::Q}, {codon::CAG, aa::Q}, - {codon::CGT, aa::R}, {codon::CGC, aa::R}, {codon::CGA, aa::R}, {codon::CGG, aa::R}, - {codon::ATT, aa::I}, {codon::ATC, aa::I}, {codon::ATA, aa::I}, {codon::ATG, aa::M}, - {codon::ACT, aa::T}, {codon::ACC, aa::T}, {codon::ACA, aa::T}, {codon::ACG, aa::T}, - {codon::AAT, aa::N}, {codon::AAC, aa::N}, {codon::AAA, aa::K}, {codon::AAG, aa::K}, - {codon::AGT, aa::S}, {codon::AGC, aa::S}, {codon::AGA, aa::R}, {codon::AGG, aa::R}, - {codon::GTT, aa::V}, {codon::GTC, aa::V}, {codon::GTA, aa::V}, {codon::GTG, aa::V}, - {codon::GCT, aa::A}, {codon::GCC, aa::A}, {codon::GCA, aa::A}, {codon::GCG, aa::A}, - {codon::GAT, aa::D}, {codon::GAC, aa::D}, {codon::GAA, aa::E}, {codon::GAG, aa::E}, - {codon::GGT, aa::G}, {codon::GGC, aa::G}, {codon::GGA, aa::G}, {codon::GGG, aa::G}, + {codon::TTT, aa_F}, {codon::TTC, aa_F}, {codon::TTA, aa_L}, {codon::TTG, aa_L}, + {codon::TCT, aa_S}, {codon::TCC, aa_S}, {codon::TCA, aa_S}, {codon::TCG, aa_S}, + {codon::TAT, aa_Y}, {codon::TAC, aa_Y}, {codon::TAA, aa_star}, {codon::TAG, aa_star}, + {codon::TGT, aa_C}, {codon::TGC, aa_C}, {codon::TGA, aa_star}, {codon::TGG, aa_W}, + {codon::CTT, aa_L}, {codon::CTC, aa_L}, {codon::CTA, aa_L}, {codon::CTG, aa_L}, + {codon::CCT, aa_P}, {codon::CCC, aa_P}, {codon::CCA, aa_P}, {codon::CCG, aa_P}, + {codon::CAT, aa_H}, {codon::CAC, aa_H}, {codon::CAA, aa_Q}, {codon::CAG, aa_Q}, + {codon::CGT, aa_R}, {codon::CGC, aa_R}, {codon::CGA, aa_R}, {codon::CGG, aa_R}, + {codon::ATT, aa_I}, {codon::ATC, aa_I}, {codon::ATA, aa_I}, {codon::ATG, aa_M}, + {codon::ACT, aa_T}, {codon::ACC, aa_T}, {codon::ACA, aa_T}, {codon::ACG, aa_T}, + {codon::AAT, aa_N}, {codon::AAC, aa_N}, {codon::AAA, aa_K}, {codon::AAG, aa_K}, + {codon::AGT, aa_S}, {codon::AGC, aa_S}, {codon::AGA, aa_R}, {codon::AGG, aa_R}, + {codon::GTT, aa_V}, {codon::GTC, aa_V}, {codon::GTA, aa_V}, {codon::GTG, aa_V}, + {codon::GCT, aa_A}, {codon::GCC, aa_A}, {codon::GCA, aa_A}, {codon::GCG, aa_A}, + {codon::GAT, aa_D}, {codon::GAC, aa_D}, {codon::GAA, aa_E}, {codon::GAG, aa_E}, + {codon::GGT, aa_G}, {codon::GGC, aa_G}, {codon::GGA, aa_G}, {codon::GGG, aa_G}, }; str2int_map aa2int { @@ -66,19 +73,19 @@ int2str_map int2aa = { }; aa2str_map aa2str = { - {aa::A,'A'}, {aa::R,'R'}, {aa::N,'N'}, {aa::D,'D'}, {aa::C,'C'}, - {aa::Q,'Q'}, {aa::E,'E'}, {aa::G,'G'}, {aa::H,'H'}, {aa::I,'I'}, - {aa::L,'L'}, {aa::K,'K'}, {aa::M,'M'}, {aa::F,'F'}, {aa::P,'P'}, - {aa::S,'S'}, {aa::T,'T'}, {aa::W,'W'}, {aa::Y,'Y'}, {aa::V,'V'}, - {aa::B,'B'}, {aa::Z,'Z'}, {aa::X,'X'}, {aa::star,'*'}, {aa::gap,'-'}, {aa::unknown,'?'} + {aa_A,'A'}, {aa_R,'R'}, {aa_N,'N'}, {aa_D,'D'}, {aa_C,'C'}, + {aa_Q,'Q'}, {aa_E,'E'}, {aa_G,'G'}, {aa_H,'H'}, {aa_I,'I'}, + {aa_L,'L'}, {aa_K,'K'}, {aa_M,'M'}, {aa_F,'F'}, {aa_P,'P'}, + {aa_S,'S'}, {aa_T,'T'}, {aa_W,'W'}, {aa_Y,'Y'}, {aa_V,'V'}, + {aa_B,'B'}, {aa_Z,'Z'}, {aa_X,'X'}, {aa_star,'*'}, {aa_gap,'-'}, {aa_unknown,'?'} }; str2aa_map str2aa = { - {'A',aa::A}, {'R',aa::R}, {'N',aa::N}, {'D',aa::D}, {'C',aa::C}, - {'Q',aa::Q}, {'E',aa::E}, {'G',aa::G}, {'H',aa::H}, {'I',aa::I}, - {'L',aa::L}, {'K',aa::K}, {'M',aa::M}, {'F',aa::F}, {'P',aa::P}, - {'S',aa::S}, {'T',aa::T}, {'W',aa::W}, {'Y',aa::Y}, {'V',aa::V}, - {'B',aa::B}, {'Z',aa::Z}, {'X',aa::X}, {'*',aa::star}, {'-',aa::gap}, {'?',aa::unknown} + {'A',aa_A}, {'R',aa_R}, {'N',aa_N}, {'D',aa_D}, {'C',aa_C}, + {'Q',aa_Q}, {'E',aa_E}, {'G',aa_G}, {'H',aa_H}, {'I',aa_I}, + {'L',aa_L}, {'K',aa_K}, {'M',aa_M}, {'F',aa_F}, {'P',aa_P}, + {'S',aa_S}, {'T',aa_T}, {'W',aa_W}, {'Y',aa_Y}, {'V',aa_V}, + {'B',aa_B}, {'Z',aa_Z}, {'X',aa_X}, {'*',aa_star}, {'-',aa_gap}, {'?',aa_unknown} }; codon2str_map codon2str = { @@ -137,12 +144,97 @@ to x2y(from x) template to x2y(from x) {return static_cast(x);} + +void getSeq2State(FILE *input, CharVector &p) +{ + char c; + char o; + + while (fscanf(input,"%c",&c)==1) { + + p.push_back(std::vector()); + (p.back()).push_back(c); + + while (fscanf(input,"%c",&o)==1) { + + if (o=='\n' || o=='\r') break; + + fscanf(input,"%c",&c); + (p.back()).push_back(c); + + } + + } + +} + int main(int argc, char *argv[]) { + FILE *f = fopen(argv[1],"r"); + if (f==NULL) { perror("could not load file"); exit(1); } + + CharVector Schar; + getSeq2State(f,Schar); + fclose(f); + + for (int i=0; i > aa2state; + for (int i=0; i()); + // expect all lines to contain the 'X' character to represent all the other amino acids + std::vector::iterator begin = Schar[i].begin(), end = Schar[i].end(); + int Xidx = std::distance(begin, std::find(begin,end,'X')); + for (int aa=aa_BEGIN; aa != aa_END; ++aa) { + std::vector::iterator it = std::find(begin,end,int2aa[aa]); + int idx; + if (it != end) { // amino acid explicitly encoded + idx = std::distance(begin,it); + } + else { // amino acid represented by 'X' + idx = Xidx; + } + // commonest amino acid goes to end + // maybe easier to subtract 1 and mod? + idx = idx==0 ? Schar[i].size()-1 : idx-1; + aa2state.back()[aa] = idx; + } + } + + for (int i = 0; i < aa2state.size(); i++) { + for (int aa=aa_BEGIN; aa != aa_END; ++aa) { + std::cout << aa2state[i][aa] << ' '; + } + std::cout << '\n'; + } + + std::vector configChar = {'A','Y'}; + std::vector config(configChar.size()); + for (int i=0; i < config.size(); i++) { + std::cout << configChar[i] << ' '; + config[i] = aa2int[configChar[i]]; + } + std::cout << '\n'; + + for (int i=0; i < config.size(); i++) { + std::cout << aa2state[i][config[i]] << ' '; + } + std::cout << '\n'; + + + + /* std::cout << x2y(5) << std::endl; std::cout << (int)(codon2aa[codon::TTT]) << std::endl; std::cout << static_cast(codon2aa[codon::TTC]) << std::endl; std::cout << aa2str[codon2aa[codon::TTC]] << std::endl; + */ //std::cout << aa2str[str2aa[int2aa[aa2int[codon2aa[str2codon["TTC"]]]]]] << std::endl; #if 0 diff --git a/snip.cpp b/snip.cpp index dde3cfd..a39157e 100644 --- a/snip.cpp +++ b/snip.cpp @@ -1,4 +1,6 @@ #include +#include +#include #include "snip.h" @@ -39,6 +41,10 @@ void getCouplings(FILE *input, Vector &p) { // Set energies based on an initial configuration +// Note: config[i] = 0 denotes the 2nd most common state, +// whereas config[i] = J[i].size() is the top state +// Also, "gauge fixing" sets field and couplings between +// the commonest states to zero. double computeEnergy(const Vector &J, const std::vector &config) { @@ -47,6 +53,8 @@ double computeEnergy(const Vector &J, const std::vector &config) { double E = 0; for (int i=0;i &config) { } +int main(int argc, char **argv) +{ + FILE* f = fopen(argv[1],"r"); + Vector J; + getCouplings(f,J); + fclose(f); + + for (int i=0; i