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/*
*
* taken from..
*
* MEGAHIT
* Copyright (C) 2014 - 2015 The University of Hong Kong & L3 Bioinformatics Limited
*
* ..cheers!
* it's GPL but we're GPL too so we're good, right? guys.. right?
*
* 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/>.
*/
/* contact: Dinghua Li <dhli@cs.hku.hk> */
#include <string>
#include <unordered_map>
#include <vector>
#include <cstdio>
#include <cassert>
#include <zlib.h>
#include "kseq.h"
using namespace std;
#ifndef KSEQ_INITED
#define KSEQ_INITED
KSEQ_INIT(gzFile, gzread)
#endif
char Comp(char c) {
switch (c) {
case 'A':
case 'a':
return 'T';
case 'C':
case 'c':
return 'G';
case 'G':
case 'g':
return 'C';
case 'T':
case 't':
return 'A';
default:
assert(false);
}
}
string RevComp(const string &s) {
string ret;
for (unsigned i = 0; i < s.length(); ++i) {
ret.push_back(Comp(s[s.length() - 1 - i]));
}
return ret;
}
string NodeName(int i, int len, double mul, bool is_rc) {
static char buf[10240];
sprintf(buf, "NODE_%d_length_%d_cov_%0.2f_ID_%d", i, len, mul, i * 2 - 1);
if (is_rc) return string(buf) + "'";
else return string(buf);
}
int main(int argc, char **argv) {
if (argc < 3) {
fprintf(stderr, "Usage: %s <contigs.fasta> <kmer_size>\n", argv[0]);
exit(1);
}
unsigned k = atoi(argv[2]) - 1; // megahit uses a different de bruijn definition as us, so it's k-1 for us
gzFile fp = gzopen(argv[1], "r");
if (fp == NULL)
{
fprintf(stderr,"cannot open file: %s ", argv[1]);
exit(1);
}
kseq_t *seq = kseq_init(fp); // kseq to read files
vector<string> ctgs;
vector<double> muls;
vector<string> node_names;
vector<string> rev_node_names;
unordered_map<string, vector<int> > start_kmer_to_id;
bool has_muls = true;
while (kseq_read(seq) >= 0) {
if (seq->seq.l < k) {
continue;
}
float mul;
// Minia has a special output, actually similar to the one this tool outputs. Let's parse it in a convenient way
for (int i = 0; i < seq->name.l; i++)
if (seq->name.s[i] == '_') seq->name.s[i] = ' ';
int osef;
static char osef_s[100];
int ret = sscanf(seq->name.s, "%s %d %s %d %s %f %s %d", &osef_s, &osef, &osef_s, &osef, &osef_s, &mul, &osef_s, &osef);
if (ret != 8 && has_muls)
{
fprintf(stderr, "unexpected format string, disabling recording of coverage. Is this a Minia contig? Header of first seq: '%s %s'\n", seq->name.s, seq->comment.s);
has_muls = false;
}
if (has_muls)
muls.push_back(mul);
ctgs.push_back(string(seq->seq.s));
}
for (int i = 0; i < (int)ctgs.size(); ++i) {
start_kmer_to_id[ctgs[i].substr(0, k)].push_back(i + 1);
start_kmer_to_id[RevComp(ctgs[i].substr(ctgs[i].length() - k))].push_back(-i - 1);
}
for (int i = 0; i < (int)ctgs.size(); ++i) {
float mul = 0;
if (has_muls)
mul = muls[i];
node_names.push_back(NodeName(i + 1, ctgs[i].length(), mul, false));
rev_node_names.push_back(NodeName(i + 1, ctgs[i].length(), mul, true));
}
for (int i = 0; i < (int)ctgs.size(); ++i) {
for (int dir = 0; dir < 2; ++dir) {
string header = dir == 0 ? node_names[i] : rev_node_names[i];
header = ">" + header;
string s = dir == 0 ? ctgs[i] : RevComp(ctgs[i]);
auto mit = start_kmer_to_id.find(s.substr(s.length() - k));
if (mit != start_kmer_to_id.end()) {
for (unsigned j = 0; j < mit->second.size(); ++j) {
if (j == 0) {
header += ":";
}
else {
header += ",";
}
if (mit->second[j] > 0) {
header += node_names[mit->second[j] - 1];
}
else {
header += rev_node_names[-mit->second[j] - 1];
}
}
}
header += ";";
printf("%s\n%s\n", header.c_str(), s.c_str());
}
}
return 0;
}
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