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Copy pathchromosome_utils.cpp
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234 lines (199 loc) · 8.31 KB
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/*
* Part of SMITHLAB software
*
* Copyright (C) 2014 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/>.
*/
#include"chromosome_utils.hpp"
#include"GenomicRegion.hpp"
#include"smithlab_os.hpp"
#include<algorithm>
#include<cassert>
#include<cctype>
#include<cmath>
#include<cstdlib>
#include<fstream>
#include<iterator>
#include<stdexcept>
#include<string>
#include<unordered_map>
#include<utility>
#include<vector>
using std::runtime_error;
using std::size;
using std::string;
using std::toupper;
using std::unordered_map;
using std::vector;
staticconstchar *digits = "0987654321";
staticconstchar *whitespace = "\t";
// define what to do if parts are missing: if no ':' or '-', is whole
// thing chrom?
voidparse_region_name(string region_name, string &chrom, size_t &start,
size_t &end) {
constsize_t colon_offset = region_name.find(":");
// get the chromosome
size_t chr_offset = region_name.find_last_of(whitespace, colon_offset);
if (chr_offset == string::npos)
chr_offset = 0;
else
chr_offset += 1;
chrom = region_name.substr(chr_offset, colon_offset - chr_offset);
// get the start
constsize_t start_end = region_name.find("-", colon_offset + 1);
const string start_string =
region_name.substr(colon_offset + 1, start_end - colon_offset + 1);
start = static_cast<size_t>(atoi(start_string.c_str()));
// get the end
constsize_t end_end = region_name.find_first_not_of(digits, start_end + 1);
const string end_string =
region_name.substr(start_end + 1, end_end - start_end - 1);
end = static_cast<size_t>(atoi(end_string.c_str()));
}
staticsize_tadjust_start_pos(constsize_t orig_start,
const string &chrom_name) {
staticconstexprdouble line_width = 50.0; // ADS: dangerous; often
// this is 80
constsize_t name_offset = chrom_name.length() + 2; // For the '>' and '\n';
constsize_t preceding_newlines =
static_cast<size_t>(std::floor(orig_start / line_width));
return orig_start + preceding_newlines + name_offset;
}
staticsize_tadjust_region_size(constsize_t orig_start,
constsize_t orig_size) {
staticconstexprdouble line_width = 50.0; // ADS: dangerous; often
// this is 80
constsize_t preceding_newlines_start =
static_cast<size_t>(std::floor(orig_start / line_width));
constsize_t preceding_newlines_end =
static_cast<size_t>(std::floor((orig_start + orig_size) / line_width));
return (orig_size + (preceding_newlines_end - preceding_newlines_start));
}
template <classT>
voidextract_regions_chrom_fasta_impl(const string &chrom_name,
const string &filename,
const vector<T> ®ions,
vector<string> &sequences) {
std::ifstream in(filename);
if (!in)
throwruntime_error("failed to open file: " + filename);
for (auto &i : regions) {
constauto orig_start_pos = i.get_start();
constauto orig_end_pos = i.get_end();
constauto orig_region_size = orig_end_pos - orig_start_pos;
constauto start_pos = adjust_start_pos(orig_start_pos, chrom_name);
constauto region_size =
adjust_region_size(orig_start_pos, orig_region_size);
assert(start_pos >= 0);
in.seekg(start_pos);
string buffer(region_size, '\0');
in.read(buffer.data(), region_size);
buffer.erase(remove(begin(buffer), end(buffer), '\n'));
transform(cbegin(buffer), cend(buffer), begin(buffer),
[](constchar x) { returntoupper(x); });
sequences.push_back(std::move(buffer));
assert(i.get_width() == size(sequences.back()));
}
}
voidextract_regions_chrom_fasta(const string &chrom_name,
const string &filename,
const vector<SimpleGenomicRegion> ®ions,
vector<string> &sequences) {
extract_regions_chrom_fasta_impl(chrom_name, filename, regions, sequences);
}
voidextract_regions_chrom_fasta(const string &chrom_name,
const string &filename,
const vector<GenomicRegion> ®ions,
vector<string> &sequences) {
extract_regions_chrom_fasta_impl(chrom_name, filename, regions, sequences);
}
voidextract_regions_fasta(const string &dirname,
const vector<GenomicRegion> ®ions_in,
vector<string> &sequences) {
staticconst string FASTA_SUFFIX(".fa");
assert(check_sorted(regions_in));
vector<string> filenames;
read_dir(dirname, filenames);
vector<vector<GenomicRegion>> regions;
separate_chromosomes(regions_in, regions);
std::unordered_map<string, size_t> chrom_regions_map;
for (size_t i = 0; i < filenames.size(); ++i)
chrom_regions_map[strip_path(filenames[i])] = i;
for (size_t i = 0; i < regions.size(); ++i) {
// GET THE RIGHT FILE
const string chrom_name(regions[i].front().get_chrom());
const string chrom_file(chrom_name + FASTA_SUFFIX);
std::unordered_map<string, size_t>::const_iterator f_idx =
chrom_regions_map.find(chrom_file);
if (f_idx == chrom_regions_map.end())
throwruntime_error("chrom not found:\t" + chrom_file);
extract_regions_chrom_fasta(chrom_name, filenames[f_idx->second],
regions[i], sequences);
}
}
voidextract_regions_fasta(const string &dirname,
const vector<SimpleGenomicRegion> ®ions_in,
vector<string> &sequences) {
staticconst string FASTA_SUFFIX(".fa");
assert(check_sorted(regions_in));
vector<string> filenames;
read_dir(dirname, filenames);
vector<vector<SimpleGenomicRegion>> regions;
separate_chromosomes(regions_in, regions);
std::unordered_map<string, size_t> chrom_regions_map;
for (size_t i = 0; i < filenames.size(); ++i)
chrom_regions_map[strip_path(filenames[i])] = i;
for (size_t i = 0; i < regions.size(); ++i) {
// GET THE RIGHT FILE
const string chrom_name(regions[i].front().get_chrom());
const string chrom_file(chrom_name + FASTA_SUFFIX);
std::unordered_map<string, size_t>::const_iterator f_idx =
chrom_regions_map.find(chrom_file);
if (f_idx == chrom_regions_map.end())
throwruntime_error("chrom not found:\t" + chrom_file);
extract_regions_chrom_fasta(chrom_name, filenames[f_idx->second],
regions[i], sequences);
}
}
voididentify_chromosomes(const string chrom_file, const string fasta_suffix,
unordered_map<string, string> &chrom_files) {
vector<string> the_files;
if (isdir(chrom_file.c_str())) {
read_dir(chrom_file, fasta_suffix, the_files);
for (size_t i = 0; i < the_files.size(); ++i)
chrom_files[strip_path_and_suffix(the_files[i])] = the_files[i];
}
else
chrom_files[strip_path_and_suffix(chrom_file)] = chrom_file;
}
voididentify_and_read_chromosomes(const string chrom_file,
const string fasta_suffix,
unordered_map<string, string> &chrom_files) {
vector<string> the_files;
if (isdir(chrom_file.c_str())) {
read_dir(chrom_file, fasta_suffix, the_files);
}
else
the_files.push_back(chrom_file);
for (size_t i = 0; i < the_files.size(); ++i) {
vector<string> names, seqs;
read_fasta_file(the_files[i], names, seqs);
for (size_t j = 0; j < names.size(); ++j)
chrom_files[names[j]] = the_files[i];
}
}