void Cnflearn::extfeature()
{
FILE *fp = NULL;
if ((fp = fopen(this->corpus.c_str(),"r")) == NULL)
{
fprintf (stderr,"Couln't open %s\n", this->corpus.c_str());
exit (1);
}
Sequence sq;
sq.setColSize(this->sqcolsize);
sq.setAllocSize(this->sqallocsize);
sq.setArraySize(this->sqarraysize);
sq.init();
this->instance = 0;
while(feof(fp) == 0)
{
MyUtil::sqread(fp,&sq,CNF_BUFSIZE);
if (sq.getRowSize() == 0)
{
continue;
}
this->extlabel(&sq);
this->extract(&sq);
this->instance++;
sq.clear();
}
fclose(fp);
}
std::pair<point,rhomb> read_points(std::istream& is,Sequence& s)
{
rhomb rh(INT_MIN,INT_MIN,INT_MIN,INT_MIN);
int xmax=0;
s.clear();
int y=0;
for(std::string str; std::getline(is,str); ++y) {
int line_xmax=0;
for(int x=0; (x=str.find_first_of('*',x))!=std::string::npos; ++x) {
s.push_back(point(x,y));
line_xmax=x;
if( x+y>rh.pp)rh.pp= x+y;
if( x-y>rh.pm)rh.pm= x-y;
if(-x+y>rh.mp)rh.mp=-x+y;
if(-x-y>rh.mm)rh.mm=-x-y;
}
if(line_xmax>xmax)xmax=line_xmax;
}
return std::make_pair(point(xmax+1,y),rh);
}
int main() {
Sequence s;
for (size_t i = 0; i < 6; ++i)
s.add(i);
s.display();
cout << "=========="<<endl;
s.reset();
for (size_t i = 0; i < 3; ++i)
s.next();
s.add(42);
s.display();
cout << "=========="<<endl;
s.reset();
for (size_t i = 0; i < 2; ++i)
s.next();
s.remove();
s.display();
cout << "=========="<<endl;
s.clear();
s.display();
cout << "=========="<<endl;
}
int main(void) {
// Test the fastareader
string filename = "/home/laozzzzz/barcode_project/reads/e_coli_10000snp.fa";
bool done = false;
bool success = false;
Sequence read;
std::unique_ptr<SequenceReader> reader(FastaReader::CreateSequenceReader(filename));
while(!success) {
reader->NextRead(read, success, done);
cout<< read.fowardSeq() <<endl;
}
read.clear();
filename = "/home/laozzzzz/barcode_project/reads/1000.fq";
done = false;
success = false;
reader.reset(FastqReader::CreateSequenceReader(filename));
while(!success) {
reader->NextRead(read, success, done);
cout<< read.fowardSeq() <<endl;
}
return 0;
}
void Cnflearn::learn(unsigned int iter, unsigned int reg)
{
if (!this->valid)
{
fprintf (stderr, "It's not initialized\n");
exit(1);
}
AllocMemdiscard cache(this->cachesize);
Sequence sq;
sq.setColSize(this->sqcolsize);
sq.setAllocSize(this->sqallocsize);
sq.setArraySize(this->sqarraysize);
sq.init();
int t = 0;
for (unsigned int i = 0; i < iter; i++)
{
FILE *fp = NULL;
if ((fp = fopen(this->corpus.c_str(), "r")) == NULL)
{
fprintf (stderr, "Couldn't open %s\n", this->corpus.c_str());
exit (1);
}
while (feof(fp) == 0)
{
MyUtil::sqread(fp, &sq, CNF_BUFSIZE);
if (sq.getRowSize() == 0)
{
continue;
}
this->decay(t++);
this->update(&sq, &cache, reg);
sq.clear();
cache.reset();
}
fclose(fp);
this->lreport(i);
}
}
void FastaReader::NextRead(Sequence &r, bool &success, bool &done) {
if (!r.empty())
r.clear();
int c;
success = false;
done = false;
// Pick off the first at
if(this->first_) {
c = fHandler_->get();
if(c != '>') {
c = fHandler_->getPastNewline();
if(c < 0) {
r.clear();success = false; done = true;
}
}
if(c != '>') {
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
assert_eq('>', c);
first_ = false;
}
// Read to the end of the id line, sticking everything after the '>'
// into *name
string& id = r.id();
while(true) {
c = fHandler_->get();
if(c < 0) {
r.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
if(c == '\n' || c == '\r') {
// Break at end of line, after consuming all \r's, \n's
while(c == '\n' || c == '\r') {
c = fHandler_->get();
if(c < 0) {
r.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
}
break;
}
if(c == '>')
continue;
id += c;
//name.append(c);
}
// fb_ now points just past the first character of a
// sequence line, and c holds the first character
BTDnaString& sbuf = r.fowardSeq();
while(true){
c = toupper(c);
if(c < 0){
r.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTA file" << std::endl;
throw 1;
}
else{
if(c == '\n' || c == '\r') {
break;
}
sbuf.append(asc2dna[c]);
c = fHandler_->get();
}
}
success = true;
done = fHandler_->eof();
is_done_ = done;
}
static void test_list_ops_non_unique_seq(
BOOST_EXPLICIT_TEMPLATE_TYPE(Sequence))
{
typedef typename Sequence::iterator iterator;
Sequence ss;
for(int i=0;i<10;++i){
ss.push_back(i);
ss.push_back(i);
ss.push_front(i);
ss.push_front(i);
} /* 9988776655443322110000112233445566778899 */
ss.unique();
CHECK_EQUAL(
ss,
{9 _ 8 _ 7 _ 6 _ 5 _ 4 _ 3 _ 2 _ 1 _ 0 _
1 _ 2 _ 3 _ 4 _ 5 _ 6 _ 7 _ 8 _ 9});
iterator it=ss.begin();
for(int j=0;j<9;++j,++it){} /* it points to o */
Sequence ss2;
ss2.splice(ss2.end(),ss,ss.begin(),it);
ss2.reverse();
ss.merge(ss2);
CHECK_EQUAL(
ss,
{0 _ 1 _ 1 _ 2 _ 2 _ 3 _ 3 _ 4 _ 4 _ 5 _ 5 _
6 _ 6 _ 7 _ 7 _ 8 _ 8 _ 9 _ 9});
ss.unique(same_integral_div<3>());
CHECK_EQUAL(ss,{0 _ 3 _ 6 _ 9});
ss.unique(same_integral_div<1>());
CHECK_EQUAL(ss,{0 _ 3 _ 6 _ 9});
/* testcases for bugs reported at
* http://lists.boost.org/boost-users/2006/09/22604.php
*/
{
Sequence ss,ss2;
ss.push_back(0);
ss2.push_back(0);
ss.splice(ss.end(),ss2,ss2.begin());
CHECK_EQUAL(ss,{0 _ 0});
BOOST_CHECK(ss2.empty());
ss.clear();
ss2.clear();
ss.push_back(0);
ss2.push_back(0);
ss.splice(ss.end(),ss2,ss2.begin(),ss2.end());
CHECK_EQUAL(ss,{0 _ 0});
BOOST_CHECK(ss2.empty());
ss.clear();
ss2.clear();
ss.push_back(0);
ss2.push_back(0);
ss.merge(ss2);
CHECK_EQUAL(ss,{0 _ 0});
BOOST_CHECK(ss2.empty());
typedef typename Sequence::value_type value_type;
ss.clear();
ss2.clear();
ss.push_back(0);
ss2.push_back(0);
ss.merge(ss2,std::less<value_type>());
CHECK_EQUAL(ss,{0 _ 0});
BOOST_CHECK(ss2.empty());
}
}
void fastqPattern::parseImp(Sequence& read,
bool& success,
bool& done){
char c;
success = false;
done = false;
// Pick off the first at
if(this->first_) {
c = this->fb_->get();
if(c != '@') {
c = this->fb_->getPastNewline();
if(c < 0) {
success = false; done = true;
}
line_num_ += 1;
}
if(c != '@') {
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
assert_eq('@', c);
first_ = false;
}
// Read to the end of the id line, sticking everything after the '@'
// into id
std::string& id = read.id();
while(true) {
c = this->fb_->get();
if(c == '@')
continue;
if(c < 0) {
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
if(c == '\n' || c == '\r') {
// Break at end of line, after consuming all \r's, \n's
while(c == '\n' || c == '\r') {
c = this->fb_->get();
if(c < 0) {
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
}
line_num_ += 1;
break;
}
id += c;
}
// fb_ now points just past the first character of a
// sequence line, and c holds the first character
//BTDnaString& sbuf = r->fowardSeq();
std::string& sequence = read.fowardSeq();
while(true){
c = toupper(c);
if(c < 0){
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
else{
if(c == '\n' || c == '\r') {
// Break at end of line, after consuming all \r's, \n's
while(c == '\n' || c == '\r') {
c = this->fb_->get();
if(c < 0) {
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
}
line_num_ += 1;
break;
}
// convert N to A
if(toupper(c) == 'N')
c = 'A';
sequence += c;
c = this->fb_->get();
}
}
assert_eq('+', c);
// skip the option sequence at '+' line
c = this->fb_->getPastNewline();
line_num_ += 1;
if(c <0){
read.clear(); success = false; done = true;
std::cerr << "Error: reads file does not look like a FASTQ file" << std::endl;
throw 1;
}
string& qual = read.quality();
while(true){
qual += c;
c = this->fb_->get();
if(c == '\n' || c == '\r')
break;
}
line_num_ += 1;
success = true;
assert(qual.length() == sequence.length());
done = fb_->eof();
}
static void test_list_ops_non_unique_seq()
{
typedef typename Sequence::iterator iterator;
Sequence ss;
for(int i=0;i<10;++i){
ss.push_back(i);
ss.push_back(i);
ss.push_front(i);
ss.push_front(i);
} /* 9988776655443322110000112233445566778899 */
ss.unique();
CHECK_EQUAL(
ss,
(9)(8)(7)(6)(5)(4)(3)(2)(1)(0)
(1)(2)(3)(4)(5)(6)(7)(8)(9));
iterator it=ss.begin();
for(int j=0;j<9;++j,++it){} /* it points to o */
Sequence ss2;
ss2.splice(ss2.end(),ss,ss.begin(),it);
ss2.reverse();
ss.merge(ss2);
CHECK_EQUAL(
ss,
(0)(1)(1)(2)(2)(3)(3)(4)(4)(5)(5)
(6)(6)(7)(7)(8)(8)(9)(9));
ss.unique(same_integral_div<3>());
CHECK_EQUAL(ss,(0)(3)(6)(9));
ss.unique(same_integral_div<1>());
CHECK_EQUAL(ss,(0)(3)(6)(9));
/* testcases for bugs reported at
* http://lists.boost.org/boost-users/2006/09/22604.php
*/
{
Sequence ss,ss2;
ss.push_back(0);
ss2.push_back(0);
ss.splice(ss.end(),ss2,ss2.begin());
CHECK_EQUAL(ss,(0)(0));
BOOST_TEST(ss2.empty());
ss.clear();
ss2.clear();
ss.push_back(0);
ss2.push_back(0);
ss.splice(ss.end(),ss2,ss2.begin(),ss2.end());
CHECK_EQUAL(ss,(0)(0));
BOOST_TEST(ss2.empty());
ss.clear();
ss2.clear();
ss.push_back(0);
ss2.push_back(0);
ss.merge(ss2);
CHECK_EQUAL(ss,(0)(0));
BOOST_TEST(ss2.empty());
typedef typename Sequence::value_type value_type;
ss.clear();
ss2.clear();
ss.push_back(0);
ss2.push_back(0);
ss.merge(ss2,std::less<value_type>());
CHECK_EQUAL(ss,(0)(0));
BOOST_TEST(ss2.empty());
}
}
int main (int argc, char **argv)
{
if (argc < 5)
{
fprintf (stderr, "template inputfile.gz colsize bound\n");
exit (1);
}
FILE *fp = NULL;
if ((fp = fopen(*(argv+1),"r")) == NULL)
{
fprintf (stderr, "Couldn't open %s\n", *(argv+1));
exit (1);
}
PoolAlloc ac(256, 1000000);
std::list<tmpl*> tmpls;
char buf[BUFSIZE];
while (fgets(buf, BUFSIZE, fp) != NULL)
{
MyUtil::chomp(buf);
if (MyUtil::IsCommentOut(buf))
{
continue;
}
tmpl *t = new tmpl(buf, &ac);
tmpls.push_back(t);
}
int fd = open(*(argv+2), O_RDONLY);
if (fd < 0)
{
fprintf (stderr, "Couldn't open %s\n",*(argv+2));
exit (1);
}
gzFile input = gzdopen(fd, GZ_MODE);
if (input == NULL)
{
fprintf (stderr, "failed to gzdopen\n");
exit (1);
}
int colsize = 0;
sscanf (*(argv+3),"%d",&colsize);
int bound = 0;
sscanf (*(argv+4),"%d",&bound);
Sequence sq;
sq.setColSize(colsize);
sq.init();
Dic features(&ac, CountUp);
while (gzgets(input, buf, BUFSIZE) != NULL)
{
MyUtil::chomp(buf);
if (MyUtil::IsEOS(buf))
{
int size = (int)sq.getRowSize();
std::list<tmpl*>::iterator it = tmpls.begin();
for (; it != tmpls.end(); it++)
{
for (int i = 0; i < size; i++)
{
char *feature = (*it)->expand(&sq,i);
//fprintf(stdout, "%s\n",feature);
features.insert(feature);
ac.release(feature);
}
}
sq.clear();
continue;
}
sq.push(buf);
}
nodeptr nil = features.getnil();
for (int i = HASHSIZE-1; i >= 0; i--)
{
nodeptr *p = features.table+i;
if (*p != nil)
{
recalldump(nil, (*p)->left, bound);
recalldump(nil, (*p)->right, bound);
}
}
if (gzclose(input) != Z_OK)
{
fprintf (stderr,"gzclose failed\n");
exit (1);
}
return 0;
}
