/* CGAT
* read and make tables
* BA -> NA
*/
static void CGAT(){
FILE *IN=NULL, *IN_b=NULL, *IN_rev=NULL;
int **table_value=NULL;
unsigned short **table_num=NULL;
int state_a2, state_b=0, state_rev;
Fasta *fst1 = fasta_new(), *fst2 = fasta_new(), *fst_rev = fasta_new();
clock_t start, start1, end0, end1, end2;
/*----- do BA and NA for each fasta-pair-----*/
/* genomeB file open */
IN_b = my_fopen_r(idata_b->seqname);
par.OUT = my_fopen_w(par.outputfile);
for(idata_b->cnt=0; idata_b->cnt < idata_b->fstnum; idata_b->cnt++){
start = clock();
/* MakeTable */
read_multifasta(IN_b, fst2, FORWARD, &state_b);
table_value = (int **)my_malloc(idata_b->blocknum[idata_b->cnt] * sizeof(int *), "table_b_value");
table_num = (unsigned short **)my_malloc(idata_b->blocknum[idata_b->cnt] * sizeof(unsigned short *), "table_b_num");
Make_SeedTable(fst2, table_value, table_num);
end0 = clock();
if(opt.debug) printf("MakeTable time: %.2f sec.\n", (double)(end0-start)/CLOCKS_PER_SEC);
IN = my_fopen_r(idata_a->seqname);
IN_rev = my_fopen_r(idata_a->seqname);
state_a2=0; state_rev=0;
for(idata_a->cnt=0; idata_a->cnt < idata_a->fstnum; idata_a->cnt++){
printf("\ngenomeA-fasta%d (%d blocks) - genomeB-fasta%d (%d blocks)\n",
idata_a->cnt+1, idata_a->blocknum[idata_a->cnt], idata_b->cnt+1, idata_b->blocknum[idata_b->cnt]);
start1 = clock();
/*--- BA: the results are stored in aln_for/rev ---*/
BA(&aln_for, table_value, table_num, FORWARD);
if(reverse) BA(&aln_rev, table_value, table_num, REVERSE);
if(idata_a->cnt == idata_a->fstnum -1) table_b_delete(table_value, table_num, idata_b->blocknum[idata_b->cnt]);
end1 = clock();
if(opt.debug) printf("BA time: %.2f sec.\n", (double)(end1-start1)/CLOCKS_PER_SEC);
/*--- (if -b is on) output BA result and skip NA ---*/
if(block){
output_BAresult();
continue;
}
/*--- NA: detailed alignmend within colonies in bl ---*/
NA(IN, fst1, fst2, &aln_for, FORWARD, &state_a2);
if(reverse) NA(IN_rev, fst_rev, fst2, &aln_rev, REVERSE, &state_rev);
end2 = clock();
if(opt.debug) printf("NA time: %.2f sec.\n", (double)(end2-end1)/CLOCKS_PER_SEC);
}
free(fst2->head);
free(fst2->body);
fclose(IN);
fclose(IN_rev);
}
if(opt.boundary) output_fastaboundary();
free(fst1); free(fst2); free(fst_rev);
fclose(IN_b);
fclose(par.OUT);
}
// generate multifasta from fasta file
multifasta* read_fasta_file (char* filename)
{
char ch;
// open file
FILE *filestream = fopen(filename, "rt");
// if file could not be opened ...
if (filestream == NULL)
{
printf("ERROR: Can not open File %s!\n", filename);
return NULL;
}
// initialize multifasta with 20 entries
multifasta* mfast = multifasta_new(20);
fasta* seq = NULL;
int newline = 1;
int header = 0;
int sequence = 0;
int comment = 0;
do
{
// read current char
ch = fgetc (filestream);
// check if line just started
if (newline)
{
// check if its just another newline
newline = (ch == '\n');
// check if it is a > (header starts)
if (ch == '>')
{
// if header => must not happen
if (header)
{
puts ("ERROR: File is not FASTA (no header after header allowed)!");
// free multifasta, close filestream and return NULL
fclose(filestream);
multifasta_delete (mfast);
return NULL;
}
// now the header follows
header = 1;
// is sequence preceeded => finish sequence and add to multifasta
if (sequence)
{
multifasta_add_fasta (mfast, seq);
fasta_add_base(seq, '\0');
sequence = 0;
}
// create new fasta struct
seq = fasta_new (MAX_LINE);
}
// if comment line is starting
else if (ch == '#')
{
comment = 1;
}
// if a base is the first character
else if (isBase(ch))
{
// if already a sequence is beeing read => just add base
if (sequence)
{
fasta_add_base(seq, ch);
}
// else start sequence
else
{
fasta_add_base(seq, ch);
sequence = 1;
// if no header preceeded => then it's not FASTA
if (!header)
{
puts("ERROR: File is not FASTA (hader missing)!");
// free multifasta, close filestream and return NULL
fclose(filestream);
multifasta_delete (mfast);
return NULL;
}
header = 0;
}
}
// if no base character within sequence;
// empty lines are ok and file may also end
else if (!newline && ch != EOF)
{
// free multifasta, close filestream and return NULL
fclose(filestream);
printf("ERROR: non-fasta conform line detected! %c is not an allowed symbol!\n", ch);
multifasta_delete (mfast);
return NULL;
}
}
// if we didn't start a newline
else
{
// check if its a newline character
newline = (ch == '\n');
// check if comment and if its a newline => now comment ends
// all other chars are ignored (because its a comment)
if (comment)
{
if (newline)
{
comment = 0;
}
}
// if reading a header
else if (header)
{
// if there is no newline => add it to sequence header
if (!newline)
fasta_add_header_char(seq, ch);
else
fasta_add_header_char(seq, '\0');
// do NOT set header = 0 (need for checking correct FASTA)
}
// thats ok because after a sequence started, there is never (header)
else if (sequence)
{
if (isBase(ch))
fasta_add_base(seq, ch);
else if (!newline && ch != EOF)
{
// free multifasta, close filestream and return NULL
fclose(filestream);
printf("ERROR: non-fasta conform line detected! %c is not an allowed symbol!\n",ch);
multifasta_delete (mfast);
return NULL;
}
}
}
} while (ch != EOF); // stop if EOF is reached
// file may not end with header or without seuqence
if (header || !sequence)
{
puts ("ERROR: File is not FASTA (sequence missing)!");
fclose(filestream);
multifasta_delete (mfast);
return NULL;
}
// finish last added sequence
multifasta_add_fasta (mfast, seq);
fasta_add_base(seq, '\0');
fclose(filestream);
return mfast;
}
