smithlab_cpp/GenomicRegion.hpp at master · smithlabcode/smithlab_cpp · GitHub

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* Part of SMITHLAB software

* University of Southern California and

* Andrew D. Smith

* Authors: Andrew D. Smith

* This program is free software: you can redistribute it and/or modify

* it under the terms of the GNU General Public License as published by

* the Free Software Foundation, either version 3 of the License, or

* (at your option) any later version.

* This program is distributed in the hope that it will be useful,

* but WITHOUT ANY WARRANTY; without even the implied warranty of

* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

* GNU General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with this program. If not, see <http://www.gnu.org/licenses/>.

#ifndef GENOMIC_REGION_HPP

#define GENOMIC_REGION_HPP

#include "smithlab_utils.hpp"

#include <algorithm>

#include <fstream>

#include <iterator>

#include <stdio.h>

#include <string>

#include <unordered_map>

#include <utility>

#include <vector>

class GenomicRegion;

typedef unsigned chrom_id_type;

class SimpleGenomicRegion {

public:

SimpleGenomicRegion() : chrom(assign_chrom("(null)")), start(0), end(0) {}

void swap(SimpleGenomicRegion &rhs) {

std::swap(chrom, rhs.chrom);

std::swap(start, rhs.start);

std::swap(end, rhs.end);

}

// Other constructors

SimpleGenomicRegion(std::string c, size_t sta, size_t e)

: chrom(assign_chrom(c)), start(sta), end(e) {}

SimpleGenomicRegion(const GenomicRegion &rhs);

SimpleGenomicRegion(const char *string_representation, const size_t len);

explicit SimpleGenomicRegion(const std::string &line)

: SimpleGenomicRegion(line.c_str(), line.length()) {}

std::string tostring() const;

// accessors

std::string get_chrom() const { return retrieve_chrom(chrom); }

size_t get_start() const { return start; }

size_t get_end() const { return end; }

size_t get_width() const { return (end > start) ? end - start : 0; }

// mutators

void set_chrom(const std::string &new_chrom) {

chrom = assign_chrom(new_chrom);

}

void set_start(size_t new_start) { start = new_start; }

void set_end(size_t new_end) { end = new_end; }

// comparison functions

bool contains(const SimpleGenomicRegion &other) const;

bool overlaps(const SimpleGenomicRegion &other) const;

size_t distance(const SimpleGenomicRegion &other) const;

bool operator<(const SimpleGenomicRegion &rhs) const;

bool less1(const SimpleGenomicRegion &rhs) const;

bool operator<=(const SimpleGenomicRegion &rhs) const;

bool operator==(const SimpleGenomicRegion &rhs) const;

bool operator!=(const SimpleGenomicRegion &rhs) const;

bool same_chrom(const SimpleGenomicRegion &other) const {

return chrom == other.chrom;

}

friend void separate_chromosomes(

const std::vector<SimpleGenomicRegion> &regions,

std::vector<std::vector<SimpleGenomicRegion>> &separated_by_chrom);

private:

static chrom_id_type assign_chrom(const std::string &c);

static std::string retrieve_chrom(chrom_id_type i);

static std::unordered_map<std::string, chrom_id_type> fw_table_in;

static std::unordered_map<chrom_id_type, std::string> fw_table_out;

// std::string chrom;

chrom_id_type chrom;

size_t start;

size_t end;

};

template <class T> T &operator>>(T &the_stream, SimpleGenomicRegion &r) {

std::string buffer;

if (getline(the_stream, buffer)) {

r = SimpleGenomicRegion(buffer);

}

return the_stream;

}

template <class T> T &operator<<(T &the_stream, const SimpleGenomicRegion &r) {

the_stream << r.tostring();

return the_stream;

}

class GenomicRegion {

public:

GenomicRegion()

: chrom(assign_chrom("(NULL)")), name("X"), start(0), end(0), score(0),

strand('+') {}

void swap(GenomicRegion &rhs) {

std::swap(chrom, rhs.chrom);

std::swap(name, rhs.name);

std::swap(start, rhs.start);

std::swap(end, rhs.end);

std::swap(score, rhs.score);

std::swap(strand, rhs.strand);

}

// Other constructors

GenomicRegion(std::string c, size_t sta, size_t e, std::string n, float sc,

char str)

: chrom(assign_chrom(c)), name(n), start(sta), end(e), score(sc),

strand(str) {}

GenomicRegion(std::string c, size_t sta, size_t e)

: chrom(assign_chrom(c)), name(std::string("X")), start(sta), end(e),

score(0.0), strand('+') {}

GenomicRegion(const char *s, const size_t len);

explicit GenomicRegion(const std::string &line)

: GenomicRegion(line.c_str(), line.length()) {}

GenomicRegion(const SimpleGenomicRegion &other)

: chrom(assign_chrom(other.get_chrom())), name("(NULL)"),

start(other.get_start()), end(other.get_end()), score(0), strand('+') {}

std::string tostring() const;

// accessors

std::string get_chrom() const { return retrieve_chrom(chrom); }

size_t get_start() const { return start; }

size_t get_end() const { return end; }

size_t get_width() const { return (end > start) ? end - start : 0; }

std::string get_name() const { return name; }

float get_score() const { return score; }

char get_strand() const { return strand; }

bool pos_strand() const { return (strand == '+'); }

bool neg_strand() const { return (strand == '-'); }

// mutators

void set_chrom(const std::string &new_chrom) {

chrom = assign_chrom(new_chrom);

}

void set_start(size_t new_start) { start = new_start; }

void set_end(size_t new_end) { end = new_end; }

void set_name(const std::string &n) { name = n; }

void set_score(float s) { score = s; }

void set_strand(char s) { strand = s; }

// comparison functions

bool contains(const GenomicRegion &other) const;

bool overlaps(const GenomicRegion &other) const;

size_t distance(const GenomicRegion &other) const;

bool operator<(const GenomicRegion &rhs) const;

bool less1(const GenomicRegion &rhs) const;

bool operator<=(const GenomicRegion &rhs) const;

bool operator!=(const GenomicRegion &rhs) const;

bool operator==(const GenomicRegion &rhs) const;

bool same_chrom(const GenomicRegion &other) const {

return chrom == other.chrom;

}

friend void separate_chromosomes(

const std::vector<GenomicRegion> &regions,

std::vector<std::vector<GenomicRegion>> &separated_by_chrom);

private:

static chrom_id_type assign_chrom(const std::string &c);

static std::string retrieve_chrom(chrom_id_type i);

static std::unordered_map<std::string, chrom_id_type> fw_table_in;

static std::unordered_map<chrom_id_type, std::string> fw_table_out;

// std::string chrom;

chrom_id_type chrom;

std::string name;

size_t start;

size_t end;

float score;

char strand;

};

template <class T> bool score_less(const T &a, const T &b) {

return a.get_score() < b.get_score();

}

template <class T> bool score_greater(const T &a, const T &b) {

return a.get_score() > b.get_score();

}

template <class T> T &operator>>(T &the_stream, GenomicRegion &r) {

std::string buffer;

if (getline(the_stream, buffer)) {

r = GenomicRegion(buffer);

}

return the_stream;

}

template <class T> T &operator<<(T &the_stream, const GenomicRegion &r) {

the_stream << r.tostring();

return the_stream;

}

template <class T, class U>

void sync_chroms(const std::vector<std::vector<T>> &stable,

std::vector<std::vector<U>> &to_sync) {

std::unordered_map<std::string, size_t> chrom_index;

for (size_t i = 0; i < stable.size(); ++i)

if (!stable[i].empty())

chrom_index[stable[i].front().get_chrom()] = i;

std::vector<std::vector<U>> syncd(stable.size());

for (size_t i = 0; i < to_sync.size(); ++i) {

if (!to_sync[i].empty()) {

std::unordered_map<std::string, size_t>::const_iterator j =

chrom_index.find(to_sync[i].front().get_chrom());

if (j != chrom_index.end())

to_sync[i].swap(syncd[j->second]);

}

syncd.swap(to_sync);

}

template <class T, class U>

void separate_regions(const std::vector<T> &big_regions,

const std::vector<U> &regions,

std::vector<std::vector<U>> &sep_regions) {

size_t rr_id = 0;

const size_t n_regions = regions.size();

const size_t n_big_regions = big_regions.size();

sep_regions.resize(n_big_regions);

for (size_t i = 0; i < n_big_regions; ++i) {

const std::string current_chrom(big_regions[i].get_chrom());

const size_t current_start = big_regions[i].get_start();

const size_t current_end = big_regions[i].get_end();

while (rr_id < n_regions && (regions[rr_id].get_chrom() < current_chrom ||

(regions[rr_id].get_chrom() == current_chrom &&

regions[rr_id].get_start() < current_start)))

++rr_id;

while (rr_id < n_regions && (regions[rr_id].get_chrom() == current_chrom &&

regions[rr_id].get_start() < current_end)) {

sep_regions[i].push_back(regions[rr_id]);

++rr_id;

}

template <class T> bool check_sorted(const std::vector<T> &regions) {

for (size_t i = 1; i < regions.size(); ++i)

if (regions[i] < regions[i - 1])

return false;

return true;

}

template <class T>

typename std::vector<T>::const_iterator

find_closest(const std::vector<T> &targets, const T &query) {

const auto closest = std::lower_bound(begin(targets), end(targets), query);

if (closest == begin(targets))

return closest;

if (closest == end(targets))

return (closest - 1);

return (query.distance(*closest) < query.distance(*(closest - 1)))

? closest

: (closest - 1);

}

template <class T>

typename std::vector<T>::iterator find_closest(std::vector<T> &regions,

const T &region) {

typename std::vector<T>::iterator closest =

lower_bound(regions.begin(), regions.end(), region);

if (closest == regions.begin())

return closest;

if (closest == regions.end())

return (closest - 1);

return (region.distance(*closest) < region.distance(*(closest - 1)))

? closest

: (closest - 1);

}

template <class T> void collapse(std::vector<T> &regions) {

typename std::vector<T>::iterator i, good = regions.begin();

for (i = regions.begin() + 1; i != regions.end(); ++i)

if (i->overlaps(*good)) {

good->set_start(std::min(i->get_start(), good->get_start()));

good->set_end(std::max(i->get_end(), good->get_end()));

}

else

*(++good) = *i;

regions.erase(++good, regions.end());

}

template <class T> T genomic_region_intersection(const T &a, const T &b) {

if (!a.overlaps(b))

return T(a.get_chrom(), 0, 0);

else if (a.contains(b))

return b;

else if (b.contains(a))

return a;

else if (a < b)

return T(a.get_chrom(), b.get_start(), a.get_end());

else

return T(a.get_chrom(), a.get_start(), b.get_end());

}

template <class T>

void genomic_region_intersection(const std::vector<T> &regions_a,

const std::vector<T> &regions_b,

std::vector<T> &regions_c) {

typename std::vector<T>::const_iterator a(regions_a.begin());

typename std::vector<T>::const_iterator a_lim(regions_a.end());

typename std::vector<T>::const_iterator b(regions_b.begin());

typename std::vector<T>::const_iterator b_lim(regions_b.end());

while (a != a_lim && b != b_lim) {

if (a->overlaps(*b))

regions_c.push_back(*b);

if (a == b) {

++a;

++b;

}

else if (*a < *b)

++a;

else

++b; // if (*b < *a)

}

template <class T>

void genomic_region_intersection_by_base(const std::vector<T> &regions_a,

const std::vector<T> &regions_b,

std::vector<T> &regions_c) {

typename std::vector<T>::const_iterator a(regions_a.begin());

typename std::vector<T>::const_iterator a_lim(regions_a.end());

typename std::vector<T>::const_iterator b(regions_b.begin());

typename std::vector<T>::const_iterator b_lim(regions_b.end());

while (a != a_lim && b != b_lim) {

if (a->overlaps(*b))

regions_c.push_back(T(a->get_chrom(),

std::max(a->get_start(), b->get_start()),

std::min(a->get_end(), b->get_end())));

if (a == b) {

++a;

++b;

}

else if (a->less1(*b))

++a;

else

++b; // if (*b < *a)

}

void ReadBEDFile(const std::string &filename,

std::vector<GenomicRegion> &regions);

void ReadBEDFile(const std::string &filename,

std::vector<SimpleGenomicRegion> &regions);

template <class T>

void WriteBEDFile(const std::string filename,

const std::vector<std::vector<T>> &regions,

std::string track_name = "") {

std::ofstream out(filename.c_str());

if (track_name.length() > 0)

out << "track name=" << track_name << std::endl;

for (typename std::vector<std::vector<T>>::const_iterator i = regions.begin();

i != regions.end(); ++i)

std::copy(i->begin(), i->end(), std::ostream_iterator<T>(out, "\n"));

out.close();

}

template <class T>

void WriteBEDFile(const std::string filename, const std::vector<T> &regions,

std::string track_name = "") {

std::ofstream out(filename.c_str());

if (track_name.length() > 0)

out << "track name=" << track_name << std::endl;

std::copy(regions.begin(), regions.end(),

std::ostream_iterator<T>(out, "\n"));

out.close();

}

template <class T> std::string assemble_region_name(const T &region) {

return (region.get_chrom() + ":" + smithlab::toa(region.get_start()) + "-" +

smithlab::toa(region.get_end()));

}

template <class T>

std::string assemble_region_name(const T &region, const std::string sep) {

return (region.get_chrom() + sep + smithlab::toa(region.get_start()) + sep +

smithlab::toa(region.get_end()));

}

#endif

smithlab_cpp/GenomicRegion.hpp at master · smithlabcode/smithlab_cpp · GitHub

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