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#define PY_SSIZE_T_CLEAN
#include "Python.h"
static const char bases[][4] = {"TTTT", /* 00 00 00 00 */
"TTTC", /* 00 00 00 01 */
"TTTA", /* 00 00 00 10 */
"TTTG", /* 00 00 00 11 */
"TTCT", /* 00 00 01 00 */
"TTCC", /* 00 00 01 01 */
"TTCA", /* 00 00 01 10 */
"TTCG", /* 00 00 01 11 */
"TTAT", /* 00 00 10 00 */
"TTAC", /* 00 00 10 01 */
"TTAA", /* 00 00 10 10 */
"TTAG", /* 00 00 10 11 */
"TTGT", /* 00 00 11 00 */
"TTGC", /* 00 00 11 01 */
"TTGA", /* 00 00 11 10 */
"TTGG", /* 00 00 11 11 */
"TCTT", /* 00 01 00 00 */
"TCTC", /* 00 01 00 01 */
"TCTA", /* 00 01 00 10 */
"TCTG", /* 00 01 00 11 */
"TCCT", /* 00 01 01 00 */
"TCCC", /* 00 01 01 01 */
"TCCA", /* 00 01 01 10 */
"TCCG", /* 00 01 01 11 */
"TCAT", /* 00 01 10 00 */
"TCAC", /* 00 01 10 01 */
"TCAA", /* 00 01 10 10 */
"TCAG", /* 00 01 10 11 */
"TCGT", /* 00 01 11 00 */
"TCGC", /* 00 01 11 01 */
"TCGA", /* 00 01 11 10 */
"TCGG", /* 00 01 11 11 */
"TATT", /* 00 10 00 00 */
"TATC", /* 00 10 00 01 */
"TATA", /* 00 10 00 10 */
"TATG", /* 00 10 00 11 */
"TACT", /* 00 10 01 00 */
"TACC", /* 00 10 01 01 */
"TACA", /* 00 10 01 10 */
"TACG", /* 00 10 01 11 */
"TAAT", /* 00 10 10 00 */
"TAAC", /* 00 10 10 01 */
"TAAA", /* 00 10 10 10 */
"TAAG", /* 00 10 10 11 */
"TAGT", /* 00 10 11 00 */
"TAGC", /* 00 10 11 01 */
"TAGA", /* 00 10 11 10 */
"TAGG", /* 00 10 11 11 */
"TGTT", /* 00 11 00 00 */
"TGTC", /* 00 11 00 01 */
"TGTA", /* 00 11 00 10 */
"TGTG", /* 00 11 00 11 */
"TGCT", /* 00 11 01 00 */
"TGCC", /* 00 11 01 01 */
"TGCA", /* 00 11 01 10 */
"TGCG", /* 00 11 01 11 */
"TGAT", /* 00 11 10 00 */
"TGAC", /* 00 11 10 01 */
"TGAA", /* 00 11 10 10 */
"TGAG", /* 00 11 10 11 */
"TGGT", /* 00 11 11 00 */
"TGGC", /* 00 11 11 01 */
"TGGA", /* 00 11 11 10 */
"TGGG", /* 00 11 11 11 */
"CTTT", /* 01 00 00 00 */
"CTTC", /* 01 00 00 01 */
"CTTA", /* 01 00 00 10 */
"CTTG", /* 01 00 00 11 */
"CTCT", /* 01 00 01 00 */
"CTCC", /* 01 00 01 01 */
"CTCA", /* 01 00 01 10 */
"CTCG", /* 01 00 01 11 */
"CTAT", /* 01 00 10 00 */
"CTAC", /* 01 00 10 01 */
"CTAA", /* 01 00 10 10 */
"CTAG", /* 01 00 10 11 */
"CTGT", /* 01 00 11 00 */
"CTGC", /* 01 00 11 01 */
"CTGA", /* 01 00 11 10 */
"CTGG", /* 01 00 11 11 */
"CCTT", /* 01 01 00 00 */
"CCTC", /* 01 01 00 01 */
"CCTA", /* 01 01 00 10 */
"CCTG", /* 01 01 00 11 */
"CCCT", /* 01 01 01 00 */
"CCCC", /* 01 01 01 01 */
"CCCA", /* 01 01 01 10 */
"CCCG", /* 01 01 01 11 */
"CCAT", /* 01 01 10 00 */
"CCAC", /* 01 01 10 01 */
"CCAA", /* 01 01 10 10 */
"CCAG", /* 01 01 10 11 */
"CCGT", /* 01 01 11 00 */
"CCGC", /* 01 01 11 01 */
"CCGA", /* 01 01 11 10 */
"CCGG", /* 01 01 11 11 */
"CATT", /* 01 10 00 00 */
"CATC", /* 01 10 00 01 */
"CATA", /* 01 10 00 10 */
"CATG", /* 01 10 00 11 */
"CACT", /* 01 10 01 00 */
"CACC", /* 01 10 01 01 */
"CACA", /* 01 10 01 10 */
"CACG", /* 01 10 01 11 */
"CAAT", /* 01 10 10 00 */
"CAAC", /* 01 10 10 01 */
"CAAA", /* 01 10 10 10 */
"CAAG", /* 01 10 10 11 */
"CAGT", /* 01 10 11 00 */
"CAGC", /* 01 10 11 01 */
"CAGA", /* 01 10 11 10 */
"CAGG", /* 01 10 11 11 */
"CGTT", /* 01 11 00 00 */
"CGTC", /* 01 11 00 01 */
"CGTA", /* 01 11 00 10 */
"CGTG", /* 01 11 00 11 */
"CGCT", /* 01 11 01 00 */
"CGCC", /* 01 11 01 01 */
"CGCA", /* 01 11 01 10 */
"CGCG", /* 01 11 01 11 */
"CGAT", /* 01 11 10 00 */
"CGAC", /* 01 11 10 01 */
"CGAA", /* 01 11 10 10 */
"CGAG", /* 01 11 10 11 */
"CGGT", /* 01 11 11 00 */
"CGGC", /* 01 11 11 01 */
"CGGA", /* 01 11 11 10 */
"CGGG", /* 01 11 11 11 */
"ATTT", /* 10 00 00 00 */
"ATTC", /* 10 00 00 01 */
"ATTA", /* 10 00 00 10 */
"ATTG", /* 10 00 00 11 */
"ATCT", /* 10 00 01 00 */
"ATCC", /* 10 00 01 01 */
"ATCA", /* 10 00 01 10 */
"ATCG", /* 10 00 01 11 */
"ATAT", /* 10 00 10 00 */
"ATAC", /* 10 00 10 01 */
"ATAA", /* 10 00 10 10 */
"ATAG", /* 10 00 10 11 */
"ATGT", /* 10 00 11 00 */
"ATGC", /* 10 00 11 01 */
"ATGA", /* 10 00 11 10 */
"ATGG", /* 10 00 11 11 */
"ACTT", /* 10 01 00 00 */
"ACTC", /* 10 01 00 01 */
"ACTA", /* 10 01 00 10 */
"ACTG", /* 10 01 00 11 */
"ACCT", /* 10 01 01 00 */
"ACCC", /* 10 01 01 01 */
"ACCA", /* 10 01 01 10 */
"ACCG", /* 10 01 01 11 */
"ACAT", /* 10 01 10 00 */
"ACAC", /* 10 01 10 01 */
"ACAA", /* 10 01 10 10 */
"ACAG", /* 10 01 10 11 */
"ACGT", /* 10 01 11 00 */
"ACGC", /* 10 01 11 01 */
"ACGA", /* 10 01 11 10 */
"ACGG", /* 10 01 11 11 */
"AATT", /* 10 10 00 00 */
"AATC", /* 10 10 00 01 */
"AATA", /* 10 10 00 10 */
"AATG", /* 10 10 00 11 */
"AACT", /* 10 10 01 00 */
"AACC", /* 10 10 01 01 */
"AACA", /* 10 10 01 10 */
"AACG", /* 10 10 01 11 */
"AAAT", /* 10 10 10 00 */
"AAAC", /* 10 10 10 01 */
"AAAA", /* 10 10 10 10 */
"AAAG", /* 10 10 10 11 */
"AAGT", /* 10 10 11 00 */
"AAGC", /* 10 10 11 01 */
"AAGA", /* 10 10 11 10 */
"AAGG", /* 10 10 11 11 */
"AGTT", /* 10 11 00 00 */
"AGTC", /* 10 11 00 01 */
"AGTA", /* 10 11 00 10 */
"AGTG", /* 10 11 00 11 */
"AGCT", /* 10 11 01 00 */
"AGCC", /* 10 11 01 01 */
"AGCA", /* 10 11 01 10 */
"AGCG", /* 10 11 01 11 */
"AGAT", /* 10 11 10 00 */
"AGAC", /* 10 11 10 01 */
"AGAA", /* 10 11 10 10 */
"AGAG", /* 10 11 10 11 */
"AGGT", /* 10 11 11 00 */
"AGGC", /* 10 11 11 01 */
"AGGA", /* 10 11 11 10 */
"AGGG", /* 10 11 11 11 */
"GTTT", /* 11 00 00 00 */
"GTTC", /* 11 00 00 01 */
"GTTA", /* 11 00 00 10 */
"GTTG", /* 11 00 00 11 */
"GTCT", /* 11 00 01 00 */
"GTCC", /* 11 00 01 01 */
"GTCA", /* 11 00 01 10 */
"GTCG", /* 11 00 01 11 */
"GTAT", /* 11 00 10 00 */
"GTAC", /* 11 00 10 01 */
"GTAA", /* 11 00 10 10 */
"GTAG", /* 11 00 10 11 */
"GTGT", /* 11 00 11 00 */
"GTGC", /* 11 00 11 01 */
"GTGA", /* 11 00 11 10 */
"GTGG", /* 11 00 11 11 */
"GCTT", /* 11 01 00 00 */
"GCTC", /* 11 01 00 01 */
"GCTA", /* 11 01 00 10 */
"GCTG", /* 11 01 00 11 */
"GCCT", /* 11 01 01 00 */
"GCCC", /* 11 01 01 01 */
"GCCA", /* 11 01 01 10 */
"GCCG", /* 11 01 01 11 */
"GCAT", /* 11 01 10 00 */
"GCAC", /* 11 01 10 01 */
"GCAA", /* 11 01 10 10 */
"GCAG", /* 11 01 10 11 */
"GCGT", /* 11 01 11 00 */
"GCGC", /* 11 01 11 01 */
"GCGA", /* 11 01 11 10 */
"GCGG", /* 11 01 11 11 */
"GATT", /* 11 10 00 00 */
"GATC", /* 11 10 00 01 */
"GATA", /* 11 10 00 10 */
"GATG", /* 11 10 00 11 */
"GACT", /* 11 10 01 00 */
"GACC", /* 11 10 01 01 */
"GACA", /* 11 10 01 10 */
"GACG", /* 11 10 01 11 */
"GAAT", /* 11 10 10 00 */
"GAAC", /* 11 10 10 01 */
"GAAA", /* 11 10 10 10 */
"GAAG", /* 11 10 10 11 */
"GAGT", /* 11 10 11 00 */
"GAGC", /* 11 10 11 01 */
"GAGA", /* 11 10 11 10 */
"GAGG", /* 11 10 11 11 */
"GGTT", /* 11 11 00 00 */
"GGTC", /* 11 11 00 01 */
"GGTA", /* 11 11 00 10 */
"GGTG", /* 11 11 00 11 */
"GGCT", /* 11 11 01 00 */
"GGCC", /* 11 11 01 01 */
"GGCA", /* 11 11 01 10 */
"GGCG", /* 11 11 01 11 */
"GGAT", /* 11 11 10 00 */
"GGAC", /* 11 11 10 01 */
"GGAA", /* 11 11 10 10 */
"GGAG", /* 11 11 10 11 */
"GGGT", /* 11 11 11 00 */
"GGGC", /* 11 11 11 01 */
"GGGA", /* 11 11 11 10 */
"GGGG", /* 11 11 11 11 */
};
static int
extract(const unsigned char* bytes, uint32_t byteSize, uint32_t start, uint32_t end, char sequence[]) {
uint32_t i;
const uint32_t size = end - start;
const uint32_t byteStart = start / 4;
const uint32_t byteEnd = (end + 3) / 4;
if (byteSize != byteEnd - byteStart) {
PyErr_Format(PyExc_RuntimeError,
"unexpected number of bytes %u (expected %u)",
byteSize, byteEnd - byteStart);
return -1;
}
start -= byteStart * 4;
if (byteStart + 1 == byteEnd) {
/* one byte only */
memcpy(sequence, &(bases[*bytes][start]), size);
}
else {
end -= byteEnd * 4;
/* end is now a negative number equal to the distance to the byte end */
memcpy(sequence, &(bases[*bytes][start]), 4 - start);
bytes++;
sequence += (4 - start);
for (i = byteStart+1; i < byteEnd-1; i++, bytes++, sequence += 4)
memcpy(sequence, bases[*bytes], 4);
memcpy(sequence, bases[*bytes], end + 4);
bytes++;
bytes -= byteSize;
}
return 0;
}
static void
applyNs(char sequence[], uint32_t start, uint32_t end, Py_buffer *nBlocks)
{
const Py_ssize_t nBlockCount = nBlocks->shape[0];
const uint32_t* const nBlockPositions = nBlocks->buf;
Py_ssize_t i;
for (i = 0; i < nBlockCount; i++) {
uint32_t nBlockStart = nBlockPositions[2*i];
uint32_t nBlockEnd = nBlockPositions[2*i+1];
if (nBlockEnd < start) continue;
if (end < nBlockStart) break;
if (nBlockStart < start) nBlockStart = start;
if (end < nBlockEnd) nBlockEnd = end;
memset(sequence + nBlockStart - start, 'N', nBlockEnd - nBlockStart);
}
}
static void
applyMask(char sequence[], uint32_t start, uint32_t end, Py_buffer* maskBlocks)
{
const Py_ssize_t maskBlockCount = maskBlocks->shape[0];
const uint32_t* const maskBlockPositions = maskBlocks->buf;
const char diff = 'a' - 'A';
Py_ssize_t i;
for (i = 0; i < maskBlockCount; i++) {
uint32_t j;
uint32_t maskBlockStart = maskBlockPositions[2*i];
uint32_t maskBlockEnd = maskBlockPositions[2*i+1];
if (maskBlockEnd < start) continue;
if (end < maskBlockStart) break;
if (maskBlockStart < start) maskBlockStart = start;
if (end < maskBlockEnd) maskBlockEnd = end;
for (j = maskBlockStart - start; j < maskBlockEnd - start; j++)
sequence[j] += diff;
}
}
static int
blocks_converter(PyObject* object, void* pointer)
{
const int flag = PyBUF_ND | PyBUF_FORMAT;
Py_buffer *view = pointer;
if (object == NULL) goto exit;
if (PyObject_GetBuffer(object, view, flag) == -1) {
PyErr_SetString(PyExc_RuntimeError, "blocks have unexpected format.");
return 0;
}
if (view->itemsize != sizeof(uint32_t)
|| (strcmp(view->format, "I") != 0 && strcmp(view->format, "L") != 0 )) {
PyErr_Format(PyExc_RuntimeError,
"blocks have incorrect data type (itemsize %zd, format %s)",
view->itemsize, view->format);
goto exit;
}
if (view->ndim != 2) {
PyErr_Format(PyExc_RuntimeError,
"blocks have incorrect rank %d (expected 2)", view->ndim);
goto exit;
}
if (view->shape[1] != 2) {
PyErr_Format(PyExc_RuntimeError,
"blocks should have two columns (found %zd)",
view->shape[1]);
goto exit;
}
return Py_CLEANUP_SUPPORTED;
exit:
PyBuffer_Release(view);
return 0;
}
static char TwoBit_convert__doc__[] = "convert twoBit data to the DNA sequence, apply blocks of N's (representing unknown sequences) and masked (lower case) blocks, and return the sequence as a bytes object";
static PyObject*
TwoBit_convert(PyObject* self, PyObject* args, PyObject* keywords)
{
const unsigned char *data;
Py_ssize_t start;
Py_ssize_t end;
Py_ssize_t step;
Py_ssize_t size;
Py_ssize_t length;
Py_buffer nBlocks;
Py_buffer maskBlocks;
PyObject *object;
char *sequence;
static char* kwlist[] = {"data", "start", "end", "step",
"nBlocks", "maskBlocks", NULL};
if (!PyArg_ParseTupleAndKeywords(args, keywords, "y#nnnO&O&", kwlist,
&data, &length, &start, &end, &step,
&blocks_converter, &nBlocks,
&blocks_converter, &maskBlocks))
return NULL;
size = (end - start) / step;
object = PyBytes_FromStringAndSize(NULL, size);
if (!object) goto exit;
sequence = PyBytes_AS_STRING(object);
if (step == 1) {
if (extract(data, length, start, end, sequence) < 0) {
Py_DECREF(object);
object = NULL;
goto exit;
}
applyNs(sequence, start, end, &nBlocks);
applyMask(sequence, start, end, &maskBlocks);
}
else {
Py_ssize_t current, i;
Py_ssize_t full_start, full_end;
char* full_sequence;
if (start <= end) {
full_start = start;
full_end = end;
current = 0; /* first position in sequence */
}
else {
full_start = end + 1;
full_end = start + 1;
current = start - end - 1; /* last position in sequence */
}
full_sequence = PyMem_Malloc((full_end-full_start+1)*sizeof(char));
full_sequence[full_end-full_start] = '\0';
if (!full_sequence) {
Py_DECREF(object);
object = NULL;
goto exit;
}
if (extract(data, length, full_start, full_end, full_sequence) < 0) {
PyMem_Free(full_sequence);
Py_DECREF(object);
object = NULL;
goto exit;
}
applyNs(full_sequence, full_start, full_end, &nBlocks);
applyMask(full_sequence, full_start, full_end, &maskBlocks);
for (i = 0; i < size; current += step, i++)
sequence[i] = full_sequence[current];
PyMem_Free(full_sequence);
}
exit:
blocks_converter(NULL, &nBlocks);
blocks_converter(NULL, &maskBlocks);
return object;
}
static struct PyMethodDef _twoBitIO_methods[] = {
{"convert",
(PyCFunction)TwoBit_convert,
METH_VARARGS | METH_KEYWORDS,
TwoBit_convert__doc__
},
{NULL, NULL, 0, NULL} /* sentinel */
};
static struct PyModuleDef moduledef = {
PyModuleDef_HEAD_INIT,
"_twoBitIO",
"Parser for DNA sequence data in 2bit format",
-1,
_twoBitIO_methods,
NULL,
NULL,
NULL,
NULL
};
PyObject *
PyInit__twoBitIO(void)
{
return PyModule_Create(&moduledef);
}
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