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// Copyright 2004 by Harry Zuzan. All rights reserved.
// This code is part of the Biopython distribution and governed by its
// license. Please see the LICENSE file that should have been included
// as part of this package.
// This source code parses an Affymetrix cel file.
//
// Documentation to come.
//
#include "Python.h"
#include "Numeric/arrayobject.h"
using namespace std;
#include <string>
#include <deque>
static PyObject * cel_parse(PyObject * self, PyObject * args)
{
char * cel_file;
int len_cel_file;
if (!PyArg_ParseTuple(args, "s#", &cel_file, &len_cel_file)) return 0;
deque<string>lines;
string tmp_str = "";
for (int i=0; i<len_cel_file; i++)
{
char c = cel_file[i];
if ( c == '\n' )
{
lines.push_back(tmp_str);
tmp_str = "";
}
else if ( c != '\r' ) tmp_str = tmp_str + c;
}
string HEADER = "[HEADER]";
while (1)
{
string line = lines.front();
lines.pop_front();
if (line == HEADER) break;
}
size_t token_pos;
token_pos = lines.front().find("=") + 1;
int ncols = atoi(string(lines.front(),token_pos).c_str());
lines.pop_front();
token_pos = lines.front().find("=") + 1;
int nrows = atoi(string(lines.front(),token_pos).c_str());
lines.pop_front();
string INTENSITY = "[INTENSITY]";
while (lines.size())
{
string line = lines.front();
lines.pop_front();
if (line == INTENSITY) break;
}
lines.pop_front();
lines.pop_front();
int dims[2] = {nrows,ncols};
PyArrayObject * mean_py = (PyArrayObject *)
PyArray_FromDims(2, dims, PyArray_DOUBLE);
PyArrayObject * stdev_py = (PyArrayObject *)
PyArray_FromDims(2, dims, PyArray_DOUBLE);
PyArrayObject * npix_py = (PyArrayObject *)
PyArray_FromDims(2, dims, PyArray_LONG);
for (int i=0; i<nrows*ncols; i++)
{
string col_str = "";
string row_str = "";
string mean_str = "";
string stdev_str = "";
string npix_str = "";
string data_str = lines.front();
lines.pop_front();
unsigned int k = 0;
while ( data_str[k] == ' ' || data_str[k] == '\t') k++;
while ( data_str[k] != ' ' && data_str[k] != '\t')
col_str += data_str[k++];
while ( data_str[k] == ' ' || data_str[k] == '\t') k++;
while ( data_str[k] != ' ' && data_str[k] != '\t')
row_str += data_str[k++];
while ( data_str[k] == ' ' || data_str[k] == '\t') k++;
while ( data_str[k] != ' ' && data_str[k] != '\t')
mean_str += data_str[k++]; k++;
while ( data_str[k] == ' ' || data_str[k] == '\t') k++;
while ( data_str[k] != ' ' && data_str[k] != '\t')
stdev_str += data_str[k++];
while ( data_str[k] == ' ' || data_str[k] == '\t') k++;
while ( k < data_str.size()) npix_str += data_str[k++];
int row = atoi(row_str.c_str());
int col = atoi(col_str.c_str());
double mean = atof(mean_str.c_str());
double stdev = atof(stdev_str.c_str());
int npix = atoi(npix_str.c_str());
((double *)mean_py->data)[ncols*row + col] = mean;
((double *)stdev_py->data)[ncols*row + col] = stdev;
((long *)npix_py->data)[ncols*row + col] = npix;
}
PyObject * returnList = PyList_New(0);
PyList_Append( returnList, (PyObject *)mean_py);
PyList_Append( returnList, (PyObject *)stdev_py);
PyList_Append( returnList, (PyObject *)npix_py);
return returnList;
}
extern "C" {
static PyMethodDef celMethods[] = {
{"parse", cel_parse, METH_VARARGS },
{NULL, NULL}
};
void init_cel()
{
Py_InitModule("_cel", celMethods);
import_array(); // need to when using Numeric Python
}
};
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