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fix reversed pam (e.g., cpf1)
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@pjb7687
pjb7687 committed Jul 29, 2021
1 parent 2405b88 commit 6ee7bad
Showing 1 changed file with 73 additions and 20 deletions.
93 changes: 73 additions & 20 deletions cas-offinder.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -329,7 +329,8 @@ void Cas_OFFinder::writeHeaders(const char* outfilename) {

void Cas_OFFinder::compareAll(const char* outfilename, bool issummary) {
unsigned int i, j, dev_index;
unsigned int bulge_size;
unsigned int bulge_size, bulge_index;
bool is_reversed_pam;
cl_ushort threshold;
string compare;
string seq_rna;
Expand Down Expand Up @@ -399,22 +400,47 @@ void Cas_OFFinder::compareAll(const char* outfilename, bool issummary) {
for (j = 0; ((j < m_chrpos.size()) && (loci >= m_chrpos[j])); j++) idx = j;
for (auto &bi: ci.second.second) {
seq_dna = string(strbuf);
if (bi.second < 0) {
is_reversed_pam = true;
bulge_index = -bi.second;
} else {
is_reversed_pam = false;
bulge_index = bi.second;
}
if (isnumeric(bi.first)) {
// dna bulge or none
bulge_size = (unsigned int)stoi(bi.first);
offset = m_dnabulgesize - bulge_size;
seq_rna = compare.substr(offset, bi.second) + string(bulge_size, '-') + compare.substr(offset + bi.second + bulge_size);
seq_dna = seq_dna.substr(offset);
if (bulge_size == 0)
if (is_reversed_pam) {
offset = 0;
seq_rna = compare.substr(0, bulge_index) + string(bulge_size, '-') + compare.substr(bulge_index + bulge_size);
} else {
offset = m_dnabulgesize - bulge_size;
seq_rna = compare.substr(offset, bulge_index) + string(bulge_size, '-') + compare.substr(offset + bulge_index + bulge_size);
seq_dna = seq_dna.substr(offset);
}
if (bulge_size == 0) {
bulge_type = "X";
else
if (is_reversed_pam) {
seq_rna = seq_rna.substr(0, seq_rna.size() - m_dnabulgesize);
seq_dna = seq_dna.substr(0, seq_dna.size() - m_dnabulgesize);
}
} else {
bulge_type = "DNA";
}
} else {
// rna bulge
bulge_size = (unsigned int)bi.first.size();
offset = m_dnabulgesize + bulge_size;
seq_rna = compare.substr(offset, bi.second) + bi.first + compare.substr(bi.second + bulge_size);
seq_dna = seq_dna.substr(offset, bi.second) + string(bulge_size, '-') + seq_dna.substr(bi.second + bulge_size);
if (is_reversed_pam) {
offset = 0;
seq_rna = compare.substr(0, bulge_index) + bi.first + compare.substr(bulge_index);
seq_dna = seq_dna.substr(0, bulge_index) + string(bulge_size, '-') + seq_dna.substr(bulge_index);
seq_rna = seq_rna.substr(0, seq_rna.size() - m_dnabulgesize - bulge_size);
seq_dna = seq_dna.substr(0, seq_dna.size() - m_dnabulgesize - bulge_size);
} else {
offset = m_dnabulgesize + bulge_size;
seq_rna = compare.substr(offset, bulge_index) + bi.first + compare.substr(offset + bulge_index);
seq_dna = seq_dna.substr(offset, bulge_index) + string(bulge_size, '-') + seq_dna.substr(offset + bulge_index);
}
bulge_type = "RNA";
}
(*fo) << id << "\t" << bulge_type << "\t" << seq_rna << "\t" << seq_dna << "\t" << m_chrnames[idx] << "\t" << loci - m_chrpos[idx] + offset << "\t" << m_directions[dev_index][i] << "\t" << m_mmcounts[dev_index][i] << "\t" << bulge_size << endl;
Expand Down Expand Up @@ -566,6 +592,8 @@ void Cas_OFFinder::parseInput(istream& input) {
m_compare_t::iterator it; // used in `add_compare`
compareinfo ci;
bulgeinfo bi;
bool is_reversed_pam = false;
string compare, tmp;

try {
if (!input.good())
Expand All @@ -584,7 +612,12 @@ void Cas_OFFinder::parseInput(istream& input) {
m_dnabulgesize = atoi(sline[1].c_str());
m_rnabulgesize = atoi(sline[2].c_str());
}
m_pattern = string(m_dnabulgesize, 'N') + sline[0];
if (sline[0][0] != 'N') { // As of today (2021.07.29), there is no reversed PAM starts with 'N'
is_reversed_pam = true;
m_pattern = sline[0] + string(m_dnabulgesize, 'N');
} else {
m_pattern = string(m_dnabulgesize, 'N') + sline[0];
}
transform(m_pattern.begin(), m_pattern.end(), m_pattern.begin(), ::toupper);

size_t linecnt = 0;
Expand All @@ -607,20 +640,40 @@ void Cas_OFFinder::parseInput(istream& input) {
else
id = to_string(linecnt);
ci = make_pair(id, threshold);
bi = make_pair("0", 0);
add_compare(string(m_dnabulgesize, 'N') + sline[0], ci, bi);
for (i = 1; i <= m_dnabulgesize; i++) {
preNcnt = m_dnabulgesize - i;
for (j = 1; j < sline[0].find_last_not_of('N') + 1; j++) {
bi = make_pair(to_string(i), j);
add_compare(string(preNcnt, 'N') + sline[0].substr(0, j) + string(i, 'N') + sline[0].substr(j), ci, bi);
if (m_dnabulgesize == 0) {
bi = make_pair("0", 0);
add_compare(sline[0], ci, bi);
} else {
if (is_reversed_pam)
tmp = sline[0] + string(m_dnabulgesize, 'N');
else
tmp = string(m_dnabulgesize, 'N') + sline[0];
for (i = 1; i <= m_dnabulgesize; i++) {
preNcnt = m_dnabulgesize - i;
for (j = sline[0].find_first_not_of('N'); j < sline[0].find_last_not_of('N') + 2; j++) {
if (is_reversed_pam) {
compare = sline[0].substr(0, j) + string(i, 'N') + sline[0].substr(j) + string(preNcnt, 'N');
} else {
compare = string(preNcnt, 'N') + sline[0].substr(0, j) + string(i, 'N') + sline[0].substr(j);
}
if (compare == tmp)
bi = make_pair("0", (is_reversed_pam?-j:j));
else
bi = make_pair(to_string(i), (is_reversed_pam?-j:j));
add_compare(compare, ci, bi);
}
}
}
for (i = 1; i <= m_rnabulgesize; i++) {
preNcnt = m_dnabulgesize + i;
for (j = 1; j < sline[0].find_last_not_of('N') + 1 - i; j++) {
bi = make_pair(sline[0].substr(j, i), j);
add_compare(string(preNcnt, 'N') + sline[0].substr(0, j) + sline[0].substr(j + i), ci, bi);
for (j = sline[0].find_first_not_of('N'); j < sline[0].find_last_not_of('N') + 1 - i; j++) {
bi = make_pair(sline[0].substr(j, i), (is_reversed_pam?-j:j));
if (is_reversed_pam) {
compare = sline[0].substr(0, j) + sline[0].substr(j + i) + string(preNcnt, 'N');
} else {
compare = string(preNcnt, 'N') + sline[0].substr(0, j) + sline[0].substr(j + i);
}
add_compare(compare, ci, bi);
}
}
if (entrycnt == 0) {
Expand Down

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