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/* This file is part of TransTerm v2.0 BETA and is covered by the GNU GPL
* License version 2.0. See file LICENSE.txt for more details. */
#include <iostream>
#include <string>
#include <sstream>
#include <cassert>
#include "gene-reader.h"
#include "util.h"
// return the right kind of annotation reader given teh extn of the filename
// if none, return 0
GeneReader *
gene_reader_factory(const string & fn)
{
string extn = fn.substr(fn.rfind('.')+1);
if(extn == "ptt") return new PTTReader(fn);
if(extn == "coords" || extn == "crd") return new CoordsReader(fn);
return 0;
}
// make a new PTTReader.
PTTReader::PTTReader(const string & fn)
: _in(fn.c_str())
{
unsigned dotpos = fn.rfind('.');
// remove the extn
_id = (dotpos == 0)?fn:fn.substr(0, dotpos);
// remove leading paths .../
_id = _id.substr(_id.rfind('/')+1);
}
// read the genes and put them into the genome
bool
PTTReader::read_genes(Genome & g)
{
string line;
assert(good());
// read the header
getline(_in, line);
getline(_in, line);
getline(_in, line);
while(getline(_in, line))
{
string loc, strand, pid, gene, syn, code, cog, desc, name;
int len;
istringstream iss(line);
iss >> loc >> strand >> len >> pid >> gene >> syn >> code >> cog;
getline(iss, desc);
desc = trim_front(desc);
if(gene != "-") name = gene;
else if(syn != "-") name = syn;
else if(pid != "-") name = pid;
else name = "UNK";
vector<string> locvec;
split(loc, '.', locvec);
if(locvec.size() != 3)
{
cerr << "Bad location format: " << loc << endl;
exit(3);
}
unsigned long start, end;
start = atol(locvec[0].c_str());
end = atol(locvec[2].c_str());
// make sure that the coords are given as left..right where left <= right
if(end < start)
{
cerr << "WARNING: TransTerm does not handle genomes with genes that wrap around."
<< endl;
continue;
}
if(strand == "-")
{
swap(start, end);
}
else if(strand != "+")
{
cerr << "Unknown strand value: " << strand << endl;
exit(3);
}
Seq * s = chrom_for_id(g, _id);
if(s)
{
if(start > s->length || end > s->length || start < 0 || end < 0)
{
cerr << "Bad gene coordinates: " << start << " - " << end << endl;
exit(3);
}
s->genes.push_back(
new Region(name, s, s->dna + start - 1, s->dna + end - 1, desc));
}
else
{
cerr << "Can't find seq for id: " << _id << endl;
exit(3);
}
}
return true;
}
// make a new reader for .coords file
CoordsReader::CoordsReader(const string & fn)
: _in(fn.c_str())
{
}
// Read the gene cords file a stream formated as:
// gene_name start end chrom_id
// where if start > end the gene runs on the other strand.
// Start and end are 1-based
bool
CoordsReader::read_genes(Genome & g)
{
assert(good());
Seq * s;
string line;
while(getline(_in, line))
{
string name, chid;
unsigned long startidx, endidx;
istringstream iss(line);
chid = "";
iss >> name >> startidx >> endidx >> chid;
// if there was no chid, we assume that its b/c we are missing
// the gene names.
if(chid == "")
{
istringstream iss(line);
iss >> startidx >> endidx >> chid;
name = "UNK";
}
s = chrom_for_id(g, chid);
if(s)
{
if(startidx > s->length || endidx > s->length ||
startidx <= 0 || endidx <= 0)
{
cerr << "Bad gene coordinates: " << startidx << " .. "
<< endidx << endl;
exit(3);
}
s->genes.push_back(
new Region(name, s, s->dna + startidx - 1, s->dna + endidx - 1));
}
else
{
cerr << "Unknown chromosome id: " << chid << endl;
exit(3);
}
}
return true;
}
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