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#include "stats.h"
void Stats::init()
{
mean_ = 0;
for (int i = 0; i < 9; i++)
{
n50_[i] = 0;
n50n_[i] = 0;
}
longest_ = 0;
shortest_ = 0;
number_ = 0;
totalLength_ = 0;
nCount_ = 0;
gapCount_ = 0;
filename_ = "";
}
Stats::Stats()
{
init();
}
Stats::Stats(string filename, unsigned long minimumLength)
{
init();
vector<int> seqLengths;
ifstream inStream;
unsigned long cumulativeLength = 0;
inStream.open(filename.c_str());
if (! inStream.is_open())
{
cerr << "Error opening file '" << filename << "'" << endl;
exit(1);
}
filename_ = filename;
short filetype = fastaOrFastq(inStream);
while(inStream.good())
{
Fasta* seq;
if (filetype == FASTQ_FILE)
{
Fastq* p;
p = new Fastq;
seq = (Fastq*) p;
}
else if (filetype == FASTA_FILE)
{
seq = new Fasta();
}
else
{
cerr << "Input file type not recognised as fasta or fastq. Aborting" << endl;
exit(1);
}
if ( !(seq->fillFromFile(inStream)) )
{
break;
}
else if (seq->length() >= minimumLength)
{
int l = seq->length();
seqLengths.push_back(l);
totalLength_ += l;
vector< pair<unsigned long, unsigned long> > gaps = seq->gaps();
gapCount_ += gaps.size();
for (vector< pair<unsigned long, unsigned long> >::iterator p = gaps.begin(); p != gaps.end(); ++p)
{
nCount_ += p->second - p->first + 1;
}
}
delete seq;
}
inStream.close();
if (seqLengths.size() == 0)
{
return;
}
sort(seqLengths.begin(), seqLengths.end());
longest_ = seqLengths.back();
shortest_ = seqLengths.front();
number_ = seqLengths.size();
mean_ = 1.0 * totalLength_ / number_;
int k = 0;
for (int i = seqLengths.size() - 1; 0 <= i; i--)
{
cumulativeLength += seqLengths[i];
while (k < 9 && cumulativeLength >= totalLength_ * (k + 1) / 10.0)
{
n50_[k] = seqLengths[i];
n50n_[k] = seqLengths.size() - i;
k++;
}
}
}
string Stats::toString(short format) const
{
switch (format)
{
case FORMAT_HUMAN:
return toString_human_readable();
case FORMAT_TAB:
return toString_tab_delimited(true);
case FORMAT_TAB_NO_HEAD:
return toString_tab_delimited(false);
case FORMAT_GREPPY:
return toString_greppy();
default:
cerr << "Wrong format supplied to Stats::toString(). Cannot continue" << endl;
exit(1);
}
}
string Stats::toString_greppy() const
{
stringstream ss;
ss.precision(2);
ss << filename_ << "\t" << "total_length\t" << totalLength_ << endl
<< filename_ << "\t" << "number\t" << number_ << endl
<< filename_ << "\t" << "mean_length\t" << fixed << mean_ << endl
<< filename_ << "\t" << "longest\t" << longest_ << endl
<< filename_ << "\t" << "shortest\t" << shortest_ << endl
<< filename_ << "\t" << "N_count\t" << nCount_ << endl
<< filename_ << "\t" << "Gaps\t" << gapCount_ << endl;
for (int j = 0; j < 9; j++)
{
ss << filename_ << "\t" << "n" << j + 1 << "0\t" << n50_[j] << endl
<< filename_ << "\t" << "n" << j + 1 << "0n\t" << n50n_[j] << endl;
}
return ss.str();
}
string Stats::toString_tab_delimited(bool header) const
{
stringstream ss;
ss.precision(2);
if (header)
{
ss << "filename"
<< '\t' << "total_length"
<< '\t' << "number"
<< '\t' << "mean_length"
<< '\t' << "longest"
<< '\t' << "shortest"
<< '\t' << "N_count"
<< '\t' << "Gaps"
<< '\t' << "N50"
<< '\t' << "N50n"
<< '\t' << "N70"
<< '\t' << "N70n"
<< '\t' << "N90"
<< '\t' << "N90n" << endl;
}
ss << filename_ << '\t'
<< totalLength_ << '\t'
<< number_ << '\t'
<< fixed << mean_ << '\t'
<< longest_ << '\t'
<< shortest_ << '\t'
<< nCount_ << '\t'
<< gapCount_;
for (int j = 4; j < 9; j+=2)
{
ss << '\t' << n50_[j] << '\t' << n50n_[j];
}
ss << endl;
return ss.str();
}
string Stats::toString_human_readable() const
{
stringstream ss;
ss.precision(2);
ss << "stats for " << filename_ << endl
<< "sum = " << totalLength_
<< ", n = " << number_
<< ", ave = " << fixed << mean_
<< ", largest = " << longest_ << endl
<< "N50 = " << n50_[4] << ", n = " << n50n_[4] << endl
<< "N60 = " << n50_[5] << ", n = " << n50n_[5] << endl
<< "N70 = " << n50_[6] << ", n = " << n50n_[6] << endl
<< "N80 = " << n50_[7] << ", n = " << n50n_[7] << endl
<< "N90 = " << n50_[8] << ", n = " << n50n_[8] << endl
<< "N100 = " << shortest_ << ", n = " << number_ << endl
<< "N_count = " << nCount_ << endl
<< "Gaps = " << gapCount_ << endl;
return ss.str();
}
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