DnaProfileNode * balanced_4_Sequence_fasta_stream(FILE * ifp)
{
Sequence * one;
Sequence * two;
Sequence * three;
Sequence * four;
DnaProfileNode * leafone;
DnaProfileNode * leaftwo;
DnaProfileNode * leafthree;
DnaProfileNode * leaffour;
DnaProfileNode * midonetwo;
DnaProfileNode * midthreefour;
DnaProfileNode * root;
one = read_fasta_Sequence(ifp);
fprintf(stderr,"Got 1 %s\n",one->name);
two = read_fasta_Sequence(ifp);
fprintf(stderr,"Got 2 %s\n",two->name);
three = read_fasta_Sequence(ifp);
fprintf(stderr,"Got 3 %s\n",three->name);
four = read_fasta_Sequence(ifp);
fprintf(stderr,"Got 4 %s\n",four->name);
assert(four != NULL);
leafone = new_leaf_DnaProfileNode(one);
leaftwo = new_leaf_DnaProfileNode(two);
leafthree = new_leaf_DnaProfileNode(three);
leaffour = new_leaf_DnaProfileNode(four);
midonetwo = DnaProfileNode_alloc();
midonetwo->type = DnaProfileNode_SET;
midonetwo->left = leafone;
midonetwo->right = leaftwo;
midthreefour = DnaProfileNode_alloc();
midthreefour->type = DnaProfileNode_SET;
midthreefour->left = leafthree;
midthreefour->right = leaffour;
root = DnaProfileNode_alloc();
root->type = DnaProfileNode_SET;
root->left = midonetwo;
root->right = midthreefour;
return root;
}
Sequence * get_Sequence_from_SequenceDB(SequenceDB * sdb,DataEntry * de)
{
FILE * ifp;
Sequence * ret;
/* actually, all our info is in dataentry */
ifp = openfile(de->filename,"r");
if( ifp == NULL ) {
warn("Bad error - could not open database file %s for reading indexed sequence",de->filename);
return NULL;
}
fseek(ifp,de->data[0],SEEK_SET);
switch(de->data[1]) {
case SEQ_DB_FASTA :
ret = read_fasta_Sequence(ifp);
break;
default :
warn("Unknown SequenceDB type [%d]",de->data[1]);
ret = NULL;
}
fclose(ifp);
return ret;
}
DnaProfileNode * simple_cascade_Sequence_fasta_stream(FILE * ifp)
{
DnaProfileNode * head;
DnaProfileNode * leaf;
DnaProfileNode * first;
DnaProfileNode * temp;
Sequence * read;
read = read_fasta_Sequence(ifp);
uppercase_Sequence(read);
if( read == NULL ) {
fatal("Attempting to build a cascade with only no sequences! impossible!");
}
first = new_leaf_DnaProfileNode(read);
read = read_fasta_Sequence(ifp);
uppercase_Sequence(read);
if( read == NULL ) {
fatal("Attempting to build a cascade with only one sequence! impossible!");
}
leaf = new_leaf_DnaProfileNode(read);
head = DnaProfileNode_alloc();
head->type = DnaProfileNode_SET;
head->left = first;
head->right = leaf;
/* now loop over all remaining sequences */
while( (read = read_fasta_Sequence(ifp)) != NULL ) {
uppercase_Sequence(read);
leaf = new_leaf_DnaProfileNode(read);
temp = DnaProfileNode_alloc();
temp->type = DnaProfileNode_SET;
temp->left = head;
temp->right = leaf;
head = temp;
}
return head;
}
Sequence * get_next_SequenceDB(SequenceDB * sdb)
{
/* remember the byte position now */
sdb->byte_position = ftell(sdb->current_file);
switch (sdb->fs[sdb->current_source]->format) {
case SEQ_DB_FASTA :
return read_fasta_Sequence(sdb->current_file);
default :
warn("Unknown SequenceDB type [%d]",sdb->fs[sdb->current_source]->format);
return NULL;
}
}
int main(int argc,char ** argv)
{
Sequence * input;
ShotgunPara p;
p.read_length = 500;
p.insert_size = 200;
p.number = 4000;
p.forward_only = 1;
input = read_fasta_Sequence(stdin);
generate_shotgun_reads(&p,input,stdout);
}
int main(int argc,char ** argv)
{
Sequence * in;
Sequence * rev;
while( in = read_fasta_Sequence(stdin) ) {
in->type = SEQUENCE_DNA;
rev = reverse_complement_Sequence(in);
write_fasta_Sequence(rev,stdout);
free_Sequence(in);
free_Sequence(rev);
}
}
int main(int argc,char ** argv)
{
char buffer[MAXLINE];
Sequence * in;
DnaNumberSequence * dns;
LinkNumberArray * lna;
LinkNumberArrayDebug lnad;
int i;
lnad.placement_stream = 10;
lnad.add_stream = 10;
lnad.extraction = 10;
lnad.ofp = stderr;
lna = new_LinkNumberArray(11);
while( (in = read_fasta_Sequence(stdin)) != NULL ) {
dns = new_DnaNumberSequence(in,11);
if( is_new_stream_LinkNumberArray(lna,&lnad,dns) == TRUE ) {
write_new_LinkStream(lna,&lnad,dns);
} else {
write_existing_LinkStream(lna,&lnad,dns);
}
}
for(i=0;i<lna->array_len;i++) {
if( lna->array[i] != NULL && (lna->array[i]->stream[0]->a == NULL || lna->array[i]->stream[0]->b == NULL) && lna->array[i]->stream[0]->have_seen == 0 ) {
in = extract_dna_LinkStream(lna->array[i]->stream[0],&lnad,lna->nmer_size);
sprintf(buffer,"Sequence_%d",i);
in->name = stringalloc(buffer);
write_fasta_Sequence(in,stdout);
}
}
}
