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/* Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved */
//! @file ErrorMotifs.h
//! @ingroup VariantCaller
//! @brief Handles motifs with high systematic error
#include "ErrorMotifs.h"
//-----------------------------------------------------
void TIonMotifSet::add_motif(string motif, const TMetaData &mdata) {
unsigned hpPos = 0;
int firstBase = -1;
while (hpPos < motif.length() && !isdigit(motif.at(hpPos))) {
if (motif.at(hpPos) != '.' && firstBase == -1)
firstBase = hpPos;
hpPos++;
}
if (hpPos == 0) {
cout << "TIonMotifSet: bad motif " << motif << endl;
return;
}
int key = get_key(motif.at(hpPos-1), atoi(&motif.at(hpPos)));
if (key >= (int)(4*MAX_HP_SIZE))
return;
int pref_length = hpPos - 1 - firstBase;
if (pref_length > motif_table.at(key).left_size)
motif_table.at(key).left_size = pref_length;
string submotif = (pref_length <= 0 ? "" : motif.substr(firstBase, pref_length));
submotif += "|";
int i = hpPos, suff_start = -1, lastBase = -1;
while (i < (int)motif.length()) {
if (!isdigit(motif.at(i)) && suff_start == -1) suff_start = i;
if (motif.at(i) != '.' && suff_start != -1) lastBase = i + 1;
i++;
}
int suff_length = lastBase - suff_start;
if (suff_length > motif_table.at(key).right_size)
motif_table.at(key).right_size = suff_length;
submotif += (suff_length <= 0 ? "" : motif.substr(suff_start, suff_length));
//cout << key << " " << submotif << " " << mdata->covered_sse << " " << mdata->covered_nonsse << endl;
add_my_motif(key, submotif, mdata, 0);
isempty = false;
}
//-----------------------------------------------------
unsigned TIonMotifSet::make_hashkey(string motif) const {
unsigned hashKey = 1;
for (unsigned i = 0;i < motif.length(); i++) {
hashKey <<= 2;
switch (motif[i]) {
case 'C': hashKey|=1; break;
case 'G': hashKey|=2; break;
case 'T': hashKey|=3; break;
}
}
return hashKey;
}
//-----------------------------------------------------
void TIonMotifSet::add_my_motif(short key, string motif, const TMetaData &mdata, unsigned pos) {
for (unsigned i = pos; i < motif.length(); i++)
if (motif.at(i) == '.') {
motif[i] = 'A'; add_my_motif(key, motif, mdata, pos + 1);
motif[i] = 'C'; add_my_motif(key, motif, mdata, pos + 1);
motif[i] = 'G'; add_my_motif(key, motif, mdata, pos + 1);
motif[i] = 'T'; add_my_motif(key, motif, mdata, pos + 1);
return;
}
//cout << key << "-" << motif << " " << mdata->covered_sse << " " << mdata->covered_nonsse << endl;
motif_table.at(key).add(make_hashkey(motif), mdata);
}
//-----------------------------------------------------
short TIonMotifSet::get_key(char hpChar, int hpSize) const {
hpSize = 4 * (hpSize - 1);
switch (hpChar) {
case 'T': hpSize++;
case 'G': hpSize++;
case 'C': hpSize++;
}
return (short)hpSize;
}
//-----------------------------------------------------
void TIonMotifSet::load_from_file(const char * fname) {
ifstream infile;
infile.open(fname);
string line;
if (!infile) {
cerr << "Unable to read " << fname << endl;
exit(1);
}
while (getline(infile, line)) {
if (line.length() > 0 && line[0] != '#') {
string::size_type pos = line.find("\t");
if (pos != string::npos) {
string motif = line.substr(0, pos);
int val[2];
int i = 0;
while (i < 2 && pos != string::npos) {
val[i++] = atoi(line.substr(pos + 1).c_str());
pos = line.find("\t", pos + 1);
}
if (i < 2) cerr << "skipping corrupted motif record " << line << endl;
else {
TMetaData mdata(val[0], val[1]);
add_motif(motif, mdata);
}
}
}
}
infile.close();
}
//-----------------------------------------------------
float TIonMotifSet::get_sse_probability(string context, unsigned err_base_pos) const {
if (err_base_pos >= context.length()) {
cout << "TIonMotifSet::get_sse_probability() position is out of context. context='" << context << "' pos=" << err_base_pos << endl;
return 0;
}
int i = err_base_pos - 1, j = err_base_pos + 1;
while (i >= 0 && context.at(i) == context.at(err_base_pos))
i--;
while (j < (int)context.length() && context.at(j) == context.at(err_base_pos))
j++;
int hpLen = (err_base_pos - 1) - i + 1 + j - (err_base_pos + 1);
int key = get_key(context.at(err_base_pos), hpLen);
float weight = 0;
if(key>=(int)(4*MAX_HP_SIZE))
return weight;
if (!(motif_table.at(key).isEmpty())) {
unsigned left_size = motif_table.at(key).left_size;
unsigned right_size = motif_table.at(key).right_size;
string prefix = i < 0 ? "" : context.substr(0, i + 1);
string suffix = j >= (int)context.length() ? "" : context.substr(j);
if (prefix.length() > left_size)
prefix = prefix.substr(prefix.length() - left_size);
if (suffix.length() > right_size)
suffix = suffix.substr(0, right_size);
//cout << prefix << " " << (char) context[err_base_pos] << hpLen << " " << suffix << endl;
TMetaData md(0, 0);
for (i = 0;i <= (int)prefix.length();i++)
for (j = 0;j <= (int)suffix.length();j++)
if (motif_table.at(key).has_hashkey(make_hashkey((i < (int)prefix.length() ? prefix.substr(i) : "") + "|" + (j > 0 ? suffix.substr(0, j) : "")), md)) {
float tmp_weight = md.calculate_probability();
if (tmp_weight > weight)
weight = tmp_weight;
}
}
return weight;
}
//-------------------------------------------------------
int test_main(const char * fname) {
TIonMotifSet mf;
string context = "GCTATGCCCGT"; //any size, but the best if prefix.lenght >= 7, and suffix.lenght >= 7
int err_base_position = 6; // zero based position of the query base (in this case first C in CCC
double pErr = mf.get_sse_probability(context, err_base_position);
cout << "context=" << context << " pos=" << err_base_position << " pErr=" << pErr << endl;
err_base_position = 7; // zero based position of the query base (in this case second C in CCC
pErr = mf.get_sse_probability(context, err_base_position);
cout << "context=" << context << " pos=" << err_base_position << " pErr=" << pErr << endl;
context = "TGGCACGT";
err_base_position = 1; // zero based position of the query base (in this case first G in GG
pErr = mf.get_sse_probability(context, err_base_position);
cout << "context=" << context << " pos=" << err_base_position << " pErr=" << pErr << endl;
// not in motif set
context = "TGGCACGT";
err_base_position = 3; // zero based position of the query base (in this case first C
pErr = mf.get_sse_probability(context, err_base_position);
cout << "context=" << context << " pos=" << err_base_position << " pErr=" << pErr << endl;
return 0;
}
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