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alignment.cpp
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alignment.cpp
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//
// C++ Implementation: alignment
//
// Description:
//
//
// Author: BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>, (C) 2008
//
// Copyright: See COPYING file that comes with this distribution
//
//
#include "alignment.h"
#include "myreader.h"
#include <numeric>
char symbols_protein[] = "ARNDCQEGHILKMFPSTWYVX"; // X for unknown AA
char symbols_dna[] = "ACGT";
char symbols_rna[] = "ACGU";
char symbols_binary[] = "01";
// genetic code from tri-nucleotides (AAA, AAC, AAG, AAT, ..., TTT) to amino-acids
// Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
// Base1: AAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTT
// Base2: AAAACCCCGGGGTTTTAAAACCCCGGGGTTTTAAAACCCCGGGGTTTTAAAACCCCGGGGTTTT
// Base3: ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
char genetic_code1[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"; // Standard
char genetic_code2[] = "KNKNTTTT*S*SMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Vertebrate Mitochondrial
char genetic_code3[] = "KNKNTTTTRSRSMIMIQHQHPPPPRRRRTTTTEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Yeast Mitochondrial
char genetic_code4[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Mold, Protozoan, etc.
char genetic_code5[] = "KNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Invertebrate Mitochondrial
char genetic_code6[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSS*CWCLFLF"; // Ciliate, Dasycladacean and Hexamita Nuclear
// note: tables 7 and 8 are not available in NCBI
char genetic_code9[] = "NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Echinoderm and Flatworm Mitochondrial
char genetic_code10[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSCCWCLFLF"; // Euplotid Nuclear
char genetic_code11[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"; // Bacterial, Archaeal and Plant Plastid
char genetic_code12[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLSLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"; // Alternative Yeast Nuclear
char genetic_code13[] = "KNKNTTTTGSGSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Ascidian Mitochondrial
char genetic_code14[] = "NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVYY*YSSSSWCWCLFLF"; // Alternative Flatworm Mitochondrial
char genetic_code15[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YQYSSSS*CWCLFLF"; // Blepharisma Nuclear
char genetic_code16[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLYSSSS*CWCLFLF"; // Chlorophycean Mitochondrial
// note: tables 17-20 are not available in NCBI
char genetic_code21[] = "NNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Trematode Mitochondrial
char genetic_code22[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLY*SSS*CWCLFLF"; // Scenedesmus obliquus mitochondrial
char genetic_code23[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWC*FLF"; // Thraustochytrium Mitochondrial
char genetic_code24[] = "KNKNTTTTSSKSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF"; // Pterobranchia mitochondrial
char genetic_code25[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSGCWCLFLF"; // Candidate Division SR1 and Gracilibacteria
const double MIN_FREQUENCY = 0.0001;
const double MIN_FREQUENCY_DIFF = 0.00001;
Alignment::Alignment()
: vector<Pattern>()
{
num_states = 0;
frac_const_sites = 0.0;
codon_table = NULL;
genetic_code = NULL;
non_stop_codon = NULL;
}
string &Alignment::getSeqName(int i) {
assert(i >= 0 && i < (int)seq_names.size());
return seq_names[i];
}
int Alignment::getSeqID(string &seq_name) {
for (int i = 0; i < getNSeq(); i++)
if (seq_name == getSeqName(i)) return i;
return -1;
}
int Alignment::getMaxSeqNameLength() {
int len = 0;
for (int i = 0; i < getNSeq(); i++)
if (getSeqName(i).length() > len)
len = getSeqName(i).length();
return len;
}
void Alignment::checkSeqName() {
ostringstream warn_str;
StrVector::iterator it;
for (it = seq_names.begin(); it != seq_names.end(); it++) {
string orig_name = (*it);
for (string::iterator i = it->begin(); i != it->end(); i++) {
if (!isalnum(*i) && (*i) != '_' && (*i) != '-' && (*i) != '.') {
(*i) = '_';
}
}
if (orig_name != (*it))
warn_str << orig_name << " -> " << (*it) << endl;
}
if (warn_str.str() != "") {
string str = "Some sequence names are changed as follows:\n";
outWarning(str + warn_str.str());
}
// now check that sequence names are different
StrVector names;
names.insert(names.begin(), seq_names.begin(), seq_names.end());
sort(names.begin(), names.end());
bool ok = true;
for (it = names.begin(); it != names.end(); it++) {
if (it+1==names.end()) break;
if (*it == *(it+1)) {
cout << "ERROR: Duplicated sequence name " << *it << endl;
ok = false;
}
}
if (!ok) outError("Please rename sequences listed above!");
/*if (verbose_mode >= VB_MIN)*/ {
int max_len = getMaxSeqNameLength()+1;
cout << "ID ";
cout.width(max_len);
cout << left << "Sequence" << " #Gap/Ambiguity" << endl;
int num_problem_seq = 0;
int total_gaps = 0;
for (int i = 0; i < seq_names.size(); i++) {
int num_gaps = getNSite() - countProperChar(i);
total_gaps += num_gaps;
double percent_gaps = ((double)num_gaps / getNSite())*100.0;
cout.width(4);
cout << i+1 << " ";
cout.width(max_len);
cout << left << seq_names[i] << " ";
cout.width(4);
cout << num_gaps << " (" << percent_gaps << "%)";
if (percent_gaps > 50) {
cout << " !!!";
num_problem_seq++;
}
cout << endl;
}
if (num_problem_seq) cout << "WARNING: " << num_problem_seq << " sequences contain more than 50% gaps/ambiguity" << endl;
cout << "**** ";
cout.width(max_len);
cout << left << "TOTAL" << " " << total_gaps << " (" << ((double)total_gaps/getNSite())/getNSeq()*100 << "%)" << endl;
}
}
int Alignment::checkIdenticalSeq()
{
int num_identical = 0;
IntVector checked;
checked.resize(getNSeq(), 0);
for (int seq1 = 0; seq1 < getNSeq(); seq1++) {
if (checked[seq1]) continue;
bool first = true;
for (int seq2 = seq1+1; seq2 < getNSeq(); seq2++) {
bool equal_seq = true;
for (iterator it = begin(); it != end(); it++)
if ((*it)[seq1] != (*it)[seq2]) {
equal_seq = false;
break;
}
if (equal_seq) {
if (first)
cerr << "WARNING: Identical sequences " << getSeqName(seq1);
cerr << ", " << getSeqName(seq2);
num_identical++;
checked[seq2] = 1;
first = false;
}
}
checked[seq1] = 1;
if (!first) cerr << endl;
}
if (num_identical)
outWarning("Some identical sequences found that should be discarded before the analysis");
return num_identical;
}
bool Alignment::isGapOnlySeq(int seq_id) {
assert(seq_id < getNSeq());
for (iterator it = begin(); it != end(); it++)
if ((*it)[seq_id] != STATE_UNKNOWN) {
return false;
}
return true;
}
Alignment *Alignment::removeGappySeq() {
IntVector keep_seqs;
int i, nseq = getNSeq();
for (i = 0; i < nseq; i++)
if (! isGapOnlySeq(i)) {
keep_seqs.push_back(i);
}
if (keep_seqs.size() == nseq)
return this;
Alignment *aln = new Alignment;
aln->extractSubAlignment(this, keep_seqs, 0);
return aln;
}
void Alignment::checkGappySeq(bool force_error) {
int nseq = getNSeq(), i;
int wrong_seq = 0;
for (i = 0; i < nseq; i++)
if (isGapOnlySeq(i)) {
cout << "ERROR: Sequence " << getSeqName(i) << " contains only gaps or missing data" << endl;
wrong_seq++;
}
if (wrong_seq) {
outError("Some sequences (see above) are problematic, please check your alignment again");
}
}
Alignment::Alignment(char *filename, char *sequence_type, InputType &intype) : vector<Pattern>() {
num_states = 0;
frac_const_sites = 0.0;
codon_table = NULL;
genetic_code = NULL;
non_stop_codon = NULL;
cout << "Reading alignment file " << filename << " ..." << endl;
intype = detectInputFile(filename);
try {
if (intype == IN_NEXUS) {
cout << "Nexus format detected" << endl;
readNexus(filename);
} else if (intype == IN_FASTA) {
cout << "Fasta format detected" << endl;
readFasta(filename, sequence_type);
} else if (intype == IN_PHYLIP) {
cout << "Phylip format detected" << endl;
readPhylip(filename, sequence_type);
} else {
outError("Unknown sequence format, please use PHYLIP, FASTA, or NEXUS format");
}
} catch (ios::failure) {
outError(ERR_READ_INPUT);
} catch (const char *str) {
outError(str);
} catch (string str) {
outError(str);
}
if (getNSeq() < 3)
outError("Alignment must have at least 3 sequences");
checkSeqName();
cout << "Alignment has " << getNSeq() << " sequences with " << getNSite() <<
" columns and " << getNPattern() << " patterns"<< endl;
checkIdenticalSeq();
//cout << "Number of character states is " << num_states << endl;
//cout << "Number of patterns = " << size() << endl;
countConstSite();
//cout << "Fraction of constant sites: " << frac_const_sites << endl;
}
int Alignment::readNexus(char *filename) {
NxsTaxaBlock *taxa_block;
NxsAssumptionsBlock *assumptions_block;
NxsDataBlock *data_block = NULL;
NxsTreesBlock *trees_block = NULL;
NxsCharactersBlock *char_block = NULL;
taxa_block = new NxsTaxaBlock();
assumptions_block = new NxsAssumptionsBlock(taxa_block);
data_block = new NxsDataBlock(taxa_block, assumptions_block);
char_block = new NxsCharactersBlock(taxa_block, assumptions_block);
trees_block = new TreesBlock(taxa_block);
MyReader nexus(filename);
nexus.Add(taxa_block);
nexus.Add(assumptions_block);
nexus.Add(data_block);
nexus.Add(char_block);
nexus.Add(trees_block);
MyToken token(nexus.inf);
nexus.Execute(token);
if (data_block->GetNTax() && char_block->GetNTax()) {
outError("I am confused since both DATA and CHARACTERS blocks were specified");
return 0;
}
if (char_block->GetNTax() == 0) { char_block = data_block; }
if (char_block->GetNTax() == 0) {
outError("No data is given in the input file");
return 0;
}
if (verbose_mode >= VB_DEBUG)
char_block->Report(cout);
extractDataBlock(char_block);
return 1;
}
void Alignment::extractDataBlock(NxsCharactersBlock *data_block) {
int nseq = data_block->GetNTax();
int nsite = data_block->GetNCharTotal();
char *symbols = NULL;
//num_states = strlen(symbols);
char char_to_state[NUM_CHAR];
char state_to_char[NUM_CHAR];
NxsCharactersBlock::DataTypesEnum data_type = (NxsCharactersBlock::DataTypesEnum)data_block->GetDataType();
if (data_type == NxsCharactersBlock::continuous) {
outError("Continuous characters not supported");
} else if (data_type == NxsCharactersBlock::dna || data_type == NxsCharactersBlock::rna ||
data_type == NxsCharactersBlock::nucleotide)
{
num_states = 4;
if (data_type == NxsCharactersBlock::rna)
symbols = symbols_rna;
else
symbols = symbols_dna;
} else if (data_type == NxsCharactersBlock::protein) {
num_states = 20;
symbols = symbols_protein;
} else {
num_states = 2;
symbols = symbols_binary;
}
memset(char_to_state, STATE_UNKNOWN, NUM_CHAR);
memset(state_to_char, '?', NUM_CHAR);
for (int i = 0; i < strlen(symbols); i++) {
char_to_state[(int)symbols[i]] = i;
state_to_char[i] = symbols[i];
}
state_to_char[(int)STATE_UNKNOWN] = '-';
int seq, site;
for (seq = 0; seq < nseq; seq++) {
seq_names.push_back(data_block->GetTaxonLabel(seq));
}
site_pattern.resize(nsite, -1);
int num_gaps_only = 0;
for (site = 0; site < nsite; site++) {
Pattern pat;
for (seq = 0; seq < nseq; seq++) {
int nstate = data_block->GetNumStates(seq, site);
if (nstate == 0)
pat += STATE_UNKNOWN;
else if (nstate == 1) {
pat += char_to_state[(int)data_block->GetState(seq, site, 0)];
} else {
assert(data_type != NxsCharactersBlock::dna || data_type != NxsCharactersBlock::rna || data_type != NxsCharactersBlock::nucleotide);
char pat_ch = 0;
for (int state = 0; state < nstate; state++) {
pat_ch |= (1 << char_to_state[(int)data_block->GetState(seq, site, state)]);
}
pat_ch += 3;
pat += pat_ch;
}
}
num_gaps_only += addPattern(pat, site);
}
if (num_gaps_only)
cout << "WARNING: " << num_gaps_only << " sites contain only gaps or ambiguous chars." << endl;
if (verbose_mode >= VB_MAX)
for (site = 0; site < size(); site++) {
for (seq = 0; seq < nseq; seq++)
cout << state_to_char[(int)(*this)[site][seq]];
cout << " " << (*this)[site].frequency << endl;
}
}
bool Alignment::addPattern(Pattern &pat, int site, int freq) {
// check if pattern contains only gaps
bool gaps_only = true;
for (Pattern::iterator it = pat.begin(); it != pat.end(); it++)
if ((*it) != STATE_UNKNOWN) {
gaps_only = false;
break;
}
if (gaps_only) {
if (verbose_mode >= VB_DEBUG)
cout << "Site " << site << " contains only gaps or ambiguous characters" << endl;
//return true;
}
PatternIntMap::iterator pat_it = pattern_index.find(pat);
if (pat_it == pattern_index.end()) { // not found
pat.frequency = freq;
pat.computeConst();
push_back(pat);
pattern_index[pat] = size()-1;
site_pattern[site] = size()-1;
} else {
int index = pat_it->second;
at(index).frequency += freq;
site_pattern[site] = index;
}
return gaps_only;
}
void Alignment::ungroupSitePattern()
{
vector<Pattern> stored_pat = (*this);
clear();
for (int i = 0; i < getNSite(); i++) {
Pattern pat = stored_pat[getPatternID(i)];
pat.frequency = 1;
push_back(pat);
site_pattern[i] = i;
}
pattern_index.clear();
}
void Alignment::regroupSitePattern(int groups, IntVector& site_group)
{
vector<Pattern> stored_pat = (*this);
IntVector stored_site_pattern = site_pattern;
clear();
site_pattern.clear();
site_pattern.resize(stored_site_pattern.size(), -1);
int count = 0;
for (int g = 0; g < groups; g++) {
pattern_index.clear();
for (int i = 0; i < site_group.size(); i++)
if (site_group[i] == g) {
count++;
Pattern pat = stored_pat[stored_site_pattern[i]];
addPattern(pat, i);
}
}
assert(count == stored_site_pattern.size());
count = 0;
for (iterator it = begin(); it != end(); it++)
count += it->frequency;
assert(count == getNSite());
pattern_index.clear();
//printPhylip("/dev/stdout");
}
/**
detect the data type of the input sequences
@param sequences vector of strings
@return the data type of the input sequences
*/
SeqType Alignment::detectSequenceType(StrVector &sequences) {
int num_nuc = 0;
int num_ungap = 0;
int num_bin = 0;
int num_alphabet = 0;
for (StrVector::iterator it = sequences.begin(); it != sequences.end(); it++)
for (string::iterator i = it->begin(); i != it->end(); i++) {
if ((*i) != '?' && (*i) != '-' && (*i) != '.' && *i != 'N' && *i != 'X') num_ungap++;
if ((*i) == 'A' || (*i) == 'C' || (*i) == 'G' || (*i) == 'T' || (*i) == 'U')
num_nuc++;
if ((*i) == '0' || (*i) == '1')
num_bin++;
if (isalnum(*i)) num_alphabet++;
}
if (((double)num_nuc) / num_ungap > 0.9)
return SEQ_DNA;
if (((double)num_bin) / num_ungap > 0.9)
return SEQ_BINARY;
if (((double)num_alphabet) / num_ungap < 0.5)
return SEQ_UNKNOWN;
return SEQ_PROTEIN;
}
void buildStateMap(char *map, SeqType seq_type) {
memset(map, STATE_INVALID, NUM_CHAR);
map[(unsigned char)'?'] = STATE_UNKNOWN;
map[(unsigned char)'-'] = STATE_UNKNOWN;
map[(unsigned char)'.'] = STATE_UNKNOWN;
switch (seq_type) {
case SEQ_BINARY:
map[(unsigned char)'0'] = 0;
map[(unsigned char)'1'] = 1;
return;
case SEQ_DNA: // DNA
case SEQ_CODON:
map[(unsigned char)'A'] = 0;
map[(unsigned char)'C'] = 1;
map[(unsigned char)'G'] = 2;
map[(unsigned char)'T'] = 3;
map[(unsigned char)'U'] = 3;
map[(unsigned char)'R'] = 1+4+3; // A or G, Purine
map[(unsigned char)'Y'] = 2+8+3; // C or T, Pyrimidine
map[(unsigned char)'N'] = STATE_UNKNOWN;
map[(unsigned char)'X'] = STATE_UNKNOWN;
map[(unsigned char)'W'] = 1+8+3; // A or T, Weak
map[(unsigned char)'S'] = 2+4+3; // G or C, Strong
map[(unsigned char)'M'] = 1+2+3; // A or C, Amino
map[(unsigned char)'K'] = 4+8+3; // G or T, Keto
map[(unsigned char)'B'] = 2+4+8+3; // C or G or T
map[(unsigned char)'H'] = 1+2+8+3; // A or C or T
map[(unsigned char)'D'] = 1+4+8+3; // A or G or T
map[(unsigned char)'V'] = 1+2+4+3; // A or G or C
return;
case SEQ_PROTEIN: // Protein
for (int i = 0; i < 20; i++)
map[(int)symbols_protein[i]] = i;
map[(int)symbols_protein[20]] = STATE_UNKNOWN;
map[(unsigned char)'B'] = 4+8+19; // N or D
map[(unsigned char)'Z'] = 32+64+19; // Q or E
return;
case SEQ_MULTISTATE:
for (int i = 0; i <= STATE_UNKNOWN; i++)
map[i] = i;
return;
default:
return;
}
}
/**
convert a raw characer state into ID, indexed from 0
@param state input raw state
@param seq_type data type (SEQ_DNA, etc.)
@return state ID
*/
char Alignment::convertState(char state, SeqType seq_type) {
if (state == '?' || state == '-' || state == '.')
return STATE_UNKNOWN;
char *loc;
switch (seq_type) {
case SEQ_BINARY:
switch (state) {
case '0':
return 0;
case '1':
return 1;
default:
return STATE_INVALID;
}
break;
case SEQ_DNA: // DNA
switch (state) {
case 'A':
return 0;
case 'C':
return 1;
case 'G':
return 2;
case 'T':
return 3;
case 'U':
return 3;
case 'R':
return 1+4+3; // A or G, Purine
case 'Y':
return 2+8+3; // C or T, Pyrimidine
case 'N':
return STATE_UNKNOWN;
case 'W':
return 1+8+3; // A or T, Weak
case 'S':
return 2+4+3; // G or C, Strong
case 'M':
return 1+2+3; // A or C, Amino
case 'K':
return 4+8+3; // G or T, Keto
case 'B':
return 2+4+8+3; // C or G or T
case 'H':
return 1+2+8+3; // A or C or T
case 'D':
return 1+4+8+3; // A or G or T
case 'V':
return 1+2+4+3; // A or G or C
default:
return STATE_INVALID; // unrecognize character
}
return state;
case SEQ_PROTEIN: // Protein
if (state == 'B') return 4+8+19;
if (state == 'Z') return 32+64+19;
loc = strchr(symbols_protein, state);
if (!loc) return STATE_INVALID; // unrecognize character
state = loc - symbols_protein;
if (state < 20)
return state;
else
return STATE_UNKNOWN;
default:
return STATE_INVALID;
}
}
char Alignment::convertState(char state) {
switch (num_states) {
case 2: return convertState(state, SEQ_BINARY);
case 4: return convertState(state, SEQ_DNA);
case 20: return convertState(state, SEQ_PROTEIN);
default: return STATE_INVALID;
}
}
char Alignment::convertStateBack(char state) {
if (state == STATE_UNKNOWN) return '-';
if (state == STATE_INVALID) return '?';
switch (num_states) {
case 2:
switch (state) {
case 0:
return '0';
case 1:
return '1';
default:
return STATE_INVALID;
}
case 4: // DNA
switch (state) {
case 0:
return 'A';
case 1:
return 'C';
case 2:
return 'G';
case 3:
return 'T';
case 1+4+3:
return 'R'; // A or G, Purine
case 2+8+3:
return 'Y'; // C or T, Pyrimidine
case 1+8+3:
return 'W'; // A or T, Weak
case 2+4+3:
return 'S'; // G or C, Strong
case 1+2+3:
return 'M'; // A or C, Amino
case 4+8+3:
return 'K'; // G or T, Keto
case 2+4+8+3:
return 'B'; // C or G or T
case 1+2+8+3:
return 'H'; // A or C or T
case 1+4+8+3:
return 'D'; // A or G or T
case 1+2+4+3:
return 'V'; // A or G or C
default:
return '?'; // unrecognize character
}
return state;
case 20: // Protein
if (state < 20)
return symbols_protein[(int)state];
else if (state == 4+8+19) return 'B';
else if (state == 32+64+19) return 'Z';
else
return '-';
default:
// unknown
return '*';
}
}
string Alignment::convertStateBackStr(char state) {
string str;
if (num_states <= 20) {
str = convertStateBack(state);
} else {
// codon data
if (state >= num_states) return "???";
assert(codon_table);
int state_back = codon_table[(int)state];
str = symbols_dna[state_back/16];
str += symbols_dna[(state_back%16)/4];
str += symbols_dna[state_back%4];
}
return str;
}
void Alignment::convertStateStr(string &str, SeqType seq_type) {
for (string::iterator it = str.begin(); it != str.end(); it++)
(*it) = convertState(*it, seq_type);
}
void Alignment::initCodon(char *sequence_type) {
// build index from 64 codons to non-stop codons
int transl_table = 1;
if (strlen(sequence_type) > 5) {
try {
transl_table = convert_int(sequence_type+5);
} catch (string str) {
outError("Wrong genetic code ", sequence_type);
}
switch (transl_table) {
case 1: genetic_code = genetic_code1; break;
case 2: genetic_code = genetic_code2; break;
case 3: genetic_code = genetic_code3; break;
case 4: genetic_code = genetic_code4; break;
case 5: genetic_code = genetic_code5; break;
case 6: genetic_code = genetic_code6; break;
case 9: genetic_code = genetic_code9; break;
case 10: genetic_code = genetic_code10; break;
case 11: genetic_code = genetic_code11; break;
case 12: genetic_code = genetic_code12; break;
case 13: genetic_code = genetic_code13; break;
case 14: genetic_code = genetic_code14; break;
case 15: genetic_code = genetic_code15; break;
case 16: genetic_code = genetic_code16; break;
case 21: genetic_code = genetic_code21; break;
case 22: genetic_code = genetic_code22; break;
case 23: genetic_code = genetic_code23; break;
case 24: genetic_code = genetic_code24; break;
case 25: genetic_code = genetic_code25; break;
default:
outError("Wrong genetic code ", sequence_type);
break;
}
} else {
genetic_code = genetic_code1;
}
assert(strlen(genetic_code) == 64);
cout << "Converting to codon sequences with genetic code " << transl_table << " ..." << endl;
int codon;
num_states = 0;
for (codon = 0; codon < strlen(genetic_code); codon++)
if (genetic_code[codon] != '*')
num_states++; // only count non-stop codons
codon_table = new char[num_states];
non_stop_codon = new char[strlen(genetic_code)];
int state = 0;
for (int codon = 0; codon < strlen(genetic_code); codon++) {
if (genetic_code[codon] != '*') {
non_stop_codon[codon] = state++;
codon_table[(int)non_stop_codon[codon]] = codon;
} else {
non_stop_codon[codon] = STATE_INVALID;
}
}
}
int Alignment::buildPattern(StrVector &sequences, char *sequence_type, int nseq, int nsite) {
int seq_id;
ostringstream err_str;
codon_table = NULL;
genetic_code = NULL;
non_stop_codon = NULL;
if (nseq != seq_names.size()) throw "Different number of sequences than specified";
/* now check that all sequence names are correct */
for (seq_id = 0; seq_id < nseq; seq_id ++) {
ostringstream err_str;
if (seq_names[seq_id] == "")
err_str << "Sequence number " << seq_id+1 << " has no names\n";
// check that all the names are different
for (int i = 0; i < seq_id; i++)
if (seq_names[i] == seq_names[seq_id])
err_str << "The sequence name " << seq_names[seq_id] << " is dupplicated\n";
}
if (err_str.str() != "")
throw err_str.str();
/* now check that all sequences have the same length */
for (seq_id = 0; seq_id < nseq; seq_id ++) {
if (sequences[seq_id].length() != nsite) {
err_str << "Sequence " << seq_names[seq_id] << " contains ";
if (sequences[seq_id].length() < nsite)
err_str << "not enough";
else
err_str << "too many";
err_str << " characters (" << sequences[seq_id].length() << ")\n";
}
}
if (err_str.str() != "")
throw err_str.str();
/* now check data type */
SeqType seq_type = SEQ_UNKNOWN;
seq_type = detectSequenceType(sequences);
switch (seq_type) {
case SEQ_BINARY:
num_states = 2;
cout << "Alignment most likely contains binary sequences" << endl;
break;
case SEQ_DNA:
num_states = 4;
cout << "Alignment most likely contains DNA/RNA sequences" << endl;
break;
case SEQ_PROTEIN:
num_states = 20;
cout << "Alignment most likely contains protein sequences" << endl;
break;
default:
if (!sequence_type)
throw "Unknown sequence type.";
}
if (sequence_type && strcmp(sequence_type,"") != 0) {
SeqType user_seq_type;
if (strcmp(sequence_type, "BIN") == 0) {
num_states = 2;
user_seq_type = SEQ_BINARY;
} else if (strcmp(sequence_type, "DNA") == 0) {
num_states = 4;
user_seq_type = SEQ_DNA;
} else if (strcmp(sequence_type, "AA") == 0) {
num_states = 20;
user_seq_type = SEQ_PROTEIN;
} else if (strcmp(sequence_type, "MULTI") == 0) {
cout << "Multi-state data with " << num_states << " alphabets" << endl;
user_seq_type = SEQ_MULTISTATE;
} else if (strncmp(sequence_type, "CODON", 5) == 0) {
if (seq_type != SEQ_DNA)
outWarning("You want to use codon models but the sequences were not detected as DNA");
seq_type = user_seq_type = SEQ_CODON;
initCodon(sequence_type);
} else
throw "Invalid sequence type.";
if (user_seq_type != seq_type && seq_type != SEQ_UNKNOWN)
outWarning("Your specified sequence type is different from the detected one");
seq_type = user_seq_type;
}
// now convert to patterns
int site, seq, num_gaps_only = 0;
char char_to_state[NUM_CHAR];
buildStateMap(char_to_state, seq_type);
Pattern pat;
pat.resize(nseq);
int step = ((seq_type == SEQ_CODON) ? 3 : 1);
if (nsite % step != 0)
outError("Number of sites is not multiple of 3");
site_pattern.resize(nsite/step, -1);
clear();
pattern_index.clear();
for (site = 0; site < nsite; site+=step) {
for (seq = 0; seq < nseq; seq++) {
//char state = convertState(sequences[seq][site], seq_type);
char state = char_to_state[(int)(sequences[seq][site])];
if (seq_type == SEQ_CODON) {
// special treatment for codon
char state2 = char_to_state[(int)(sequences[seq][site+1])];
char state3 = char_to_state[(int)(sequences[seq][site+2])];
if (state < 4 && state2 < 4 && state3 < 4) {
state = non_stop_codon[state*16 + state2*4 + state3];
if (state == STATE_INVALID) {
err_str << "Sequence " << seq_names[seq] << " has stop codon " <<
sequences[seq][site] << sequences[seq][site+1] << sequences[seq][site+2] <<
" at site " << site+1 << endl;
state = STATE_UNKNOWN;
}
} else if (state == STATE_INVALID || state2 == STATE_INVALID || state3 == STATE_INVALID) {
state = STATE_INVALID;
} else {
if (state != STATE_UNKNOWN || state2 != STATE_UNKNOWN || state3 != STATE_UNKNOWN) {
ostringstream warn_str;
warn_str << "Sequence " << seq_names[seq] << " has ambiguous character " <<
sequences[seq][site] << sequences[seq][site+1] << sequences[seq][site+2] <<
" at site " << site+1 << endl;
outWarning(warn_str.str());
}
state = STATE_UNKNOWN;
}
}
if (state == STATE_INVALID) {
err_str << "Sequence " << seq_names[seq] << " has invalid character " << sequences[seq][site];
if (seq_type == SEQ_CODON) err_str << sequences[seq][site+1] << sequences[seq][site+2];
err_str << " at site " << site+1 << endl;
}
pat[seq] = state;
}
num_gaps_only += addPattern(pat, site/step);
}
if (num_gaps_only)
cout << "WARNING: " << num_gaps_only << " sites contain only gaps or ambiguous chars." << endl;
if (err_str.str() != "")
throw err_str.str();
return 1;
}
int Alignment::readPhylip(char *filename, char *sequence_type) {
StrVector sequences;
ostringstream err_str;
ifstream in;
int line_num = 1;
// set the failbit and badbit
in.exceptions(ios::failbit | ios::badbit);
in.open(filename);
int nseq = 0, nsite = 0;
int seq_id = 0;
string line;
// remove the failbit
in.exceptions(ios::badbit);
bool multi_state = (sequence_type && strcmp(sequence_type,"MULTI") == 0);
num_states = 0;
for (; !in.eof(); line_num++) {
getline(in, line);
if (line == "") continue;
//cout << line << endl;
if (nseq == 0) { // read number of sequences and sites
istringstream line_in(line);
if (!(line_in >> nseq >> nsite))
throw "Invalid PHYLIP format. First line must contain number of sequences and sites";
//cout << "nseq: " << nseq << " nsite: " << nsite << endl;
if (nseq < 3)
throw "There must be at least 3 sequences";
if (nsite < 1)
throw "No alignment columns";
seq_names.resize(nseq, "");
sequences.resize(nseq, "");
} else { // read sequence contents
if (seq_names[seq_id] == "") { // cut out the sequence name
string::size_type pos = line.find(' ');
if (pos == string::npos) pos = 10; // assume standard phylip
seq_names[seq_id] = line.substr(0, pos);
line.erase(0, pos);
}
int old_len = sequences[seq_id].length();
if (multi_state) {
stringstream linestr(line);
int state;
while (!linestr.eof() ) {
state = -1;
linestr >> state;
if (state < 0) break;
sequences[seq_id].append(1, state);
if (num_states < state+1) num_states = state+1;
}
} else
for (string::iterator it = line.begin(); it != line.end(); it++) {
if ((*it) <= ' ') continue;
if (isalnum(*it) || (*it) == '-' || (*it) == '?'|| (*it) == '.')
sequences[seq_id].append(1, toupper(*it));
else {
err_str << "Unrecognized character " << *it << " on line " << line_num;
throw err_str.str();
}
}
if (sequences[seq_id].length() != sequences[0].length()) {
err_str << "Line " << line_num << ": alignment block has variable sequence lengths" << endl;
throw err_str.str();
}
if (sequences[seq_id].length() > old_len)
seq_id++;
if (seq_id == nseq) {
seq_id = 0;
// make sure that all sequences have the same length at this moment
}
}
//sequences.
}
in.clear();
// set the failbit again
in.exceptions(ios::failbit | ios::badbit);
in.close();
return buildPattern(sequences, sequence_type, nseq, nsite);
}
int Alignment::readFasta(char *filename, char *sequence_type) {
StrVector sequences;
ostringstream err_str;
ifstream in;
int line_num = 1;
string line;
// set the failbit and badbit
in.exceptions(ios::failbit | ios::badbit);
in.open(filename);
// remove the failbit
in.exceptions(ios::badbit);
for (; !in.eof(); line_num++) {
getline(in, line);
if (line == "") continue;
//cout << line << endl;
if (line[0] == '>') { // next sequence
string::size_type pos = line.find(' ');
seq_names.push_back(line.substr(1, pos-1));
sequences.push_back("");
continue;
}
// read sequence contents
if (sequences.empty()) throw "First line must begin with '>' to define sequence name";