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/* (C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */
/* blimps.c: main module of the BLIMPS blocks searcher. */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */
#define EXTERN
/* system headers not in global.h */
#include <math.h>
#include <signal.h>
/* blimps headers */
#include <global.h>
#include <version.h>
#include <residues.h>
#include <files.h>
#include <blocks.h> /* includes sequences.h, output.h */
#include <matrix.h> /* includes pattern.h */
#include <convert.h>
#include <frequency.h>
#include <options.h>
/* headers in current directory */
#include "blimps.h"
#include "blimps-mem.h"
#include "config.h"
#include "scores.h"
#include "scoring.h" /* for Alignments_Done and Scores_Done */
#include "lists.h"
/*
* Exported variables and data structures
*/
/* variables set by the configuration file */
int StrandsToSearch;
int NumberToReport;
int SearchType;
int SequenceType;
Boolean RepeatsAllowed;
Boolean SavedScoresFlag;
int GeneticCodeInitializer;
int SiteSpecificScoringMatrixType;
int BlockToMatrixConversionMethod; /* default method is two */
int SequenceMatrixScoringMethod; /* default method is zero */
/*
* Local variables and data structures
*/
static Block *block;
static Matrix *matrix;
static Sequence *sequence;
static Sequence *trans1, *trans2, *trans3;
/* translated DNA reading frames */
static Sequence *trans_1, *trans_2, *trans_3;
/* translated DNA reading frames */
static unsigned char gcode[64], revgcode[64];
/* genetic codes for translation */
static int records_searched;
/*
* sequence_vs_blocks
* When SearchType is BLOCK, there is one sequence against a blocks
* database.
* Parameters:
* FILE *emfp: the file to output the matrix information to.
* Error codes:
*/
static void sequence_vs_blocks(emfp)
FILE *emfp;
{
char prev_number[20];
/* make sure we are at the beginning of the sequence data */
rewind_file(SEQUENCE_FILES);
/* read in the first sequence (if there are others, won't be processed */
sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type());
if (sequence == NULL) {
sprintf(ErrorBuffer,
"Unable to read the sequence for scoring against the blocks.");
ErrorReport(SERIOUS_ERR_LVL);
return;
}
if (sequence->length <= 0) {
sprintf(ErrorBuffer,
"Query sequence has zero length, not scoring it.\n");
ErrorReport(SERIOUS_ERR_LVL);
return;
}
/* Just translate the query sequence once */
/* May take too much memory for long DNA sequences ... */
trans1 = trans2 = trans3 = trans_1 = trans_2 = trans_3 = NULL;
if (sequence->type == NA_SEQ)
{
if (StrandsToSearch > 0)
{
trans1 = translate_sequence(sequence, 1, gcode, revgcode);
trans2 = translate_sequence(sequence, 2, gcode, revgcode);
trans3 = translate_sequence(sequence, 3, gcode, revgcode);
}
if (StrandsToSearch < 0 || StrandsToSearch == 2)
{
trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
}
}
if (NumberToReport == 0) {
NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence);
}
/* inform what sequence the search is being done with */
/* Trying to speed things up ...
sprintf(ErrorBuffer,
"Searching sequence %s against the blocks database.\n",
sequence->name);
ErrorReport(INFO_ERR_LVL);
*/
records_searched = 0;
/* make sure we are at the begining of the block data */
rewind_file(BLOCK_FILES);
/* ------------------------loop through all the blocks */
prev_number[0] = '\0';
/* Assuming the database is correctly formatted */
while ((block = read_a_block_faster(get_file(BLOCK_FILES))) != NULL)
{
/* inform which block scoring against */
/* Trying to speed things up ...
sprintf(ErrorBuffer, "Scoring vs block %s.\n", block->number);
ErrorReport(INFO_ERR_LVL);
*/
/* Check for new family
if ((int) strlen(prev_number) < 7 ||
strncmp(block->number, prev_number, 7) != 0)
{
strcpy(prev_number, block->number);
}
*/
/* Compute a PSSM from the block */
matrix = block_to_matrix(block, BlockToMatrixConversionMethod);
if (emfp != NULL) { output_matrix(matrix, emfp); }
/* score and enter the data into the list */
/*>>>>NOTE: just call default_scoring_method() instead of
score_and_enter() since no other methods are implemented
<<<<<< */
if (sequence->type == NA_SEQ)
{
if (StrandsToSearch > 0)
{
/*
score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
*/
default_scoring_method(trans1, matrix, 1, RepeatsAllowed, SearchType, FALSE);
default_scoring_method(trans2, matrix, 2, RepeatsAllowed, SearchType, FALSE);
default_scoring_method(trans3, matrix, 3, RepeatsAllowed, SearchType, FALSE);
}
if (StrandsToSearch < 0 || StrandsToSearch == 2)
{
/*
score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
*/
default_scoring_method(trans_1, matrix, -1, RepeatsAllowed, SearchType, FALSE);
default_scoring_method(trans_2, matrix, -2, RepeatsAllowed, SearchType, FALSE);
default_scoring_method(trans_3, matrix, -3, RepeatsAllowed, SearchType, FALSE);
}
}
else /* AA */
{
/*
score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
*/
default_scoring_method(sequence, matrix, 0, RepeatsAllowed, SearchType, FALSE);
}
records_searched++;
free_block(block);
free_matrix(matrix);
} /* end while there are blocks */
if (sequence->type == NA_SEQ)
{
if (trans1 != NULL) free_sequence(trans1);
if (trans2 != NULL) free_sequence(trans2);
if (trans3 != NULL) free_sequence(trans3);
if (trans_1 != NULL) free_sequence(trans_1);
if (trans_2 != NULL) free_sequence(trans_2);
if (trans_3 != NULL) free_sequence(trans_3);
}
/* free(sequence); This is a global var, used later !!! */
} /* end of sequence_vs_blocks */
/*
* block_vs_sequences
* When SearchType is MATRIX, there is one block against a sequences
* database.
* Parameters:
* FILE *emfp: the file to output the matrix information to.
* Error codes:
*/
static void block_vs_sequences(emfp)
FILE *emfp;
{
/* make sure we are at the begining of the block data */
rewind_file(BLOCK_FILES);
/* loop through all the blocks (one) */
block = read_a_block(get_file(BLOCK_FILES));
if (block == NULL) {
sprintf(ErrorBuffer,
"Unable to read block for scoring against the sequences.");
ErrorReport(SERIOUS_ERR_LVL);
sprintf(ErrorBuffer,
"Not scoring the block.\n");
ErrorReport(SERIOUS_ERR_LVL);
return;
}
if (NumberToReport == 0) {
NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT(block);
}
/* inform what block the search is being done with */
sprintf(ErrorBuffer,
"Searching block %s against the sequence database.\n",
block->number);
ErrorReport(INFO_ERR_LVL);
/* get the block matrix */
matrix = block_to_matrix(block, BlockToMatrixConversionMethod);
if (emfp != NULL) {
output_matrix(matrix, emfp);
}
/* make sure we are at the beginning of the sequence data */
rewind_file(SEQUENCE_FILES);
records_searched = 0;
/* loop through all the sequences */
while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type())) != NULL) {
/* inform which sequence scoring against */
sprintf(ErrorBuffer,
"Scoring vs sequence %s.\n",
sequence->name);
ErrorReport(INFO_ERR_LVL);
/* is the sequence a NA_SEQ? if so, translate */
if (sequence->type == NA_SEQ) {
/* Search forward direction */
if (StrandsToSearch > 0)
{
/* translate */
trans1 = translate_sequence(sequence, 1, gcode, revgcode);
/* score and enter the data into the list */
score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
/* free the translated sequences */
free_sequence(trans1);
trans2 = translate_sequence(sequence, 2, gcode, revgcode);
score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
free_sequence(trans2);
trans3 = translate_sequence(sequence, 3, gcode, revgcode);
score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
free_sequence(trans3);
}
/* Search reverse direction */
if (StrandsToSearch == 2 || StrandsToSearch < 0)
{
trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
free_sequence(trans_1);
trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
free_sequence(trans_2);
trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
free_sequence(trans_3);
}
} /* end of NA_SEQ */
/* otherwise, just use the sequence, assuming it is an AA_SEQ */
else {
/* score and enter the data into the list */
score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
}
free_sequence(sequence);
records_searched++;
} /* end while there are sequences */
free_block(block);
free_matrix(matrix);
} /* end of block_vs_sequences */
/*
* blocks_vs_sequences
* When SearchType is UNKNOWN, there is probably a blocks database against
* a sequences database. Score all pairwise matches of blocks and
* sequences.
* Parameters:
* FILE *emfp: the file to output the matrix information to.
* Error codes:
*/
static void blocks_vs_sequences(emfp)
FILE *emfp;
{
/* NOTE: If there are speed problems, might look at the SearchType */
/* variable in files.c to see which of sequences or blocks is */
/* considered the database. The one that is the database is most */
/* likely to have the most elements, and should be in the outer */
/* loop to reduce "block->matrix" and "if NA_SEQ; NA_SEQ->AA_SEQ" */
/* overhead. */
/* set the number to report */
if (NumberToReport == 0) {
rewind_file(BLOCK_FILES);
block = read_a_block(get_file(BLOCK_FILES));
rewind_file(SEQUENCE_FILES);
sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type());
if (block == NULL) {
if (sequence == NULL) {
/* there are no comparisons to do */
NumberToReport = 1;
}
else {
NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence);
free_sequence(sequence);
}
}
else {
if (sequence == NULL) {
/* there are no comparisons to do */
NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT(block);
free_block(block);
}
else {
NumberToReport =
max((DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence)),
(DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT(block)));
free_block(block);
free_sequence(sequence);
}
}
rewind_file(BLOCK_FILES);
rewind_file(SEQUENCE_FILES);
}
/* make sure we are at the begining of the block data */
rewind_file(BLOCK_FILES);
/* loop through all the blocks */
while ((block = read_a_block(get_file(BLOCK_FILES))) != NULL) {
/* get the block matrix */
matrix = block_to_matrix(block, BlockToMatrixConversionMethod);
if (emfp != NULL) {
output_matrix_s(matrix, emfp, FLOAT_OUTPUT);
}
/* make sure we are at the beginning of the sequence data */
rewind_file(SEQUENCE_FILES);
/* loop through all the sequences */
while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type())) != NULL) {
/* inform which block and sequence are being scored */
sprintf(ErrorBuffer,
"Scoring sequence %s vs block %s.\n",
sequence->name, block->number);
ErrorReport(INFO_ERR_LVL);
/* is the sequence a NA_SEQ? if so, translate */
if (sequence->type == NA_SEQ) {
/* translate */
trans1 = translate_sequence(sequence, 1, gcode, revgcode);
trans2 = translate_sequence(sequence, 2, gcode, revgcode);
trans3 = translate_sequence(sequence, 3, gcode, revgcode);
/* score and enter the data into the list */
score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
/* free the translated sequences */
free_sequence(trans1);
free_sequence(trans2);
free_sequence(trans3);
/* if we are supposed to search both strands, translate and score */
if (StrandsToSearch == 2) {
/* translate */
trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
/* score and enter the data into the list */
score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
/* free the translated sequences */
free_sequence(trans_1);
free_sequence(trans_2);
free_sequence(trans_3);
}
}
/* otherwise, just use the sequence, assuming it is an AA_SEQ */
else {
/* score and enter the data into the list */
score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
}
free_sequence(sequence);
records_searched++;
} /* end while there are sequences */
free_block(block);
free_matrix(matrix);
} /* end while there are blocks */
} /* end of blocks_vs_sequences */
/*
* sequence_vs_matrices
* When SearchType is BLOCK, there is one sequence against a matrix
* database.
* Parameters:
* FILE *emfp: the file to output the matrix information to.
* Error codes:
*/
static void sequence_vs_matrices(emfp)
FILE *emfp;
{
/* make sure we are at the beginning of the sequence data */
rewind_file(SEQUENCE_FILES);
/* loop through all the sequences (one) */
sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type());
if (sequence == NULL) {
sprintf(ErrorBuffer,
"Unable to read the sequence for scoring against the matrices.");
ErrorReport(SERIOUS_ERR_LVL);
sprintf(ErrorBuffer,
"Not scoring the sequence.\n");
ErrorReport(SERIOUS_ERR_LVL);
return;
}
if (NumberToReport == 0) {
NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence);
}
/* inform what sequence the search is being done with */
sprintf(ErrorBuffer,
"Searching sequence %s against the matrices database.\n",
sequence->name);
ErrorReport(INFO_ERR_LVL);
records_searched = 0;
/* is the sequence a NA_SEQ? if so, translate and score */
if (sequence->type == NA_SEQ) {
/* translate */
trans1 = translate_sequence(sequence, 1, gcode, revgcode);
trans2 = translate_sequence(sequence, 2, gcode, revgcode);
trans3 = translate_sequence(sequence, 3, gcode, revgcode);
/* if we are supposed to search both strands, translate and score */
if (StrandsToSearch == 2) {
/* translate */
trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
} /* end if StrandsToSearch == 2 */
/* make sure we are at the begining of the matrix data */
rewind_file(MATRIX_FILES);
if (StrandsToSearch != 2) {
/* loop through all the matrices */
while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
/* inform which matrix scoring against */
sprintf(ErrorBuffer,
"Scoring vs matrix %s.\n",
matrix->number);
ErrorReport(INFO_ERR_LVL);
if (emfp != NULL) {
output_matrix(matrix, emfp);
}
/* score and enter the data into the list */
score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
records_searched++;
free_matrix(matrix);
} /* end while there are matrices */
}
else { /* StrandsToSearch == 2 */
/* loop through all the matrices */
while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
/* inform which matrix scoring against */
sprintf(ErrorBuffer,
"Scoring vs matrix %s.\n",
matrix->number);
ErrorReport(INFO_ERR_LVL);
if (emfp != NULL) {
output_matrix(matrix, emfp);
}
/* score and enter the data into the list */
score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
records_searched++;
free_matrix(matrix);
} /* end while there are matrices */
}
} /* end if NA_SEQ */
/* otherwise, just use the sequence, assuming it is an AA_SEQ */
else {
/* make sure we are at the begining of the matrix data */
rewind_file(MATRIX_FILES);
/* loop through all the matrices */
while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
/* inform which matrix scoring against */
sprintf(ErrorBuffer,
"Scoring vs matrix %s.\n",
matrix->number);
ErrorReport(INFO_ERR_LVL);
if (emfp != NULL) {
output_matrix(matrix, emfp);
}
/* score and enter the data into the list */
score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
records_searched++;
free_matrix(matrix);
} /* end while there are matrices */
} /* end else assuming an AA_SEQ */
/* free(sequence); This is a global var. & is used later !!*/
} /* end of sequence_vs_matrices */
/*
* matrix_vs_sequences
* When SearchType is MATRIX, there is one matrix against a sequences
* database.
* Parameters:
* FILE *emfp: the file to output the matrix information to.
* Error codes:
*/
static void matrix_vs_sequences(emfp)
FILE *emfp;
{
/* make sure we are at the begining of the matrix data */
rewind_file(MATRIX_FILES);
/* loop through all the matrices (one) */
matrix = read_a_matrix(get_file(MATRIX_FILES));
if (matrix == NULL) {
sprintf(ErrorBuffer,
"Unable to read matrix for scoring against the sequences.");
ErrorReport(SERIOUS_ERR_LVL);
sprintf(ErrorBuffer,
"Not scoring the matrix.\n");
ErrorReport(SERIOUS_ERR_LVL);
return;
}
if (NumberToReport == 0) {
NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT_M(matrix);
}
/* inform what matrix the search is being done with */
sprintf(ErrorBuffer,
"Searching matrix %s against the sequence database.\n",
matrix->number);
ErrorReport(INFO_ERR_LVL);
/* output the matrix */
if (emfp != NULL) {
output_matrix(matrix, emfp);
}
/* make sure we are at the beginning of the sequence data */
rewind_file(SEQUENCE_FILES);
records_searched = 0;
/* loop through all the sequences */
while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type())) != NULL) {
/* inform which sequence scoring against */
sprintf(ErrorBuffer,
"Scoring vs sequence %s.\n",
sequence->name);
ErrorReport(INFO_ERR_LVL);
/* is the sequence a NA_SEQ? if so, translate */
if (sequence->type == NA_SEQ) {
/* translate */
trans1 = translate_sequence(sequence, 1, gcode, revgcode);
trans2 = translate_sequence(sequence, 2, gcode, revgcode);
trans3 = translate_sequence(sequence, 3, gcode, revgcode);
/* score and enter the data into the list */
score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
/* free the translated sequences */
free_sequence(trans1);
free_sequence(trans2);
free_sequence(trans3);
/* if we are supposed to search both strands, translate and score */
if (StrandsToSearch == 2) {
/* translate */
trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
/* score and enter the data into the list */
score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
/* free the translated sequences */
free_sequence(trans_1);
free_sequence(trans_2);
free_sequence(trans_3);
}
}
/* otherwise, just use the sequence, assuming it is an AA_SEQ */
else {
/* score and enter the data into the list */
score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
}
free_sequence(sequence);
records_searched++;
} /* end while there are sequences */
free_matrix(matrix);
}
/*
* matrices_vs_sequences
* When SearchType is UNKNOWN, there is probably a matrices database against
* a sequences database. Score all pairwise matches of matrices and
* sequences.
* Parameters:
* FILE *emfp: the file to output the matrix information to.
* Error codes:
*/
static void matrices_vs_sequences(emfp)
FILE *emfp;
{
/* NOTE: If there are speed problems, might look at the SearchType */
/* variable in files.c to see which of sequences or blocks is */
/* considered the database. The one that is the database is most */
/* likely to have the most elements, and should be in the outer */
/* loop to reduce "block->matrix" and "if NA_SEQ; NA_SEQ->AA_SEQ" */
/* overhead. */
/* set the number to report */
if (NumberToReport == 0) {
rewind_file(MATRIX_FILES);
matrix = read_a_matrix(get_file(MATRIX_FILES));
rewind_file(SEQUENCE_FILES);
sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type());
if (matrix == NULL) {
if (sequence == NULL) {
/* there are no comparisons to do */
NumberToReport = 1;
}
else {
NumberToReport = DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence);
free_sequence(sequence);
}
}
else {
if (sequence == NULL) {
/* there are no comparisons to do */
NumberToReport = DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT_M(matrix);
free_matrix(matrix);
}
else {
NumberToReport =
max((DEFAULT_BLOCK_SEARCH_NUMBER_TO_REPORT(sequence)),
(DEFAULT_MATRIX_SEARCH_NUMBER_TO_REPORT_M(matrix)));
free_block(matrix);
free_sequence(sequence);
}
}
rewind_file(MATRIX_FILES);
rewind_file(SEQUENCE_FILES);
}
/* make sure we are at the begining of the matrix data */
rewind_file(MATRIX_FILES);
/* loop through all the matrices */
while ((matrix = read_a_matrix(get_file(MATRIX_FILES))) != NULL) {
/* output the matrix */
if (emfp != NULL) {
output_matrix(matrix, emfp);
}
/* make sure we are at the beginning of the sequence data */
rewind_file(SEQUENCE_FILES);
/* loop through all the sequences */
while ((sequence = read_a_sequence(get_file(SEQUENCE_FILES),
get_sequence_db_db_type(),
get_sequence_db_seq_type())) != NULL) {
/* inform which matrix and sequence are being scored */
sprintf(ErrorBuffer,
"Scoring sequence %s vs matrix %s.\n",
sequence->name, matrix->number);
ErrorReport(INFO_ERR_LVL);
/* is the sequence a NA_SEQ? if so, translate */
if (sequence->type == NA_SEQ) {
/* translate */
trans1 = translate_sequence(sequence, 1, gcode, revgcode);
trans2 = translate_sequence(sequence, 2, gcode, revgcode);
trans3 = translate_sequence(sequence, 3, gcode, revgcode);
/* score and enter the data into the list */
score_and_enter(trans1, matrix, 1, RepeatsAllowed, SearchType);
score_and_enter(trans2, matrix, 2, RepeatsAllowed, SearchType);
score_and_enter(trans3, matrix, 3, RepeatsAllowed, SearchType);
/* free the translated sequences */
free_sequence(trans1);
free_sequence(trans2);
free_sequence(trans3);
/* if we are supposed to search both strands, translate and score */
if (StrandsToSearch == 2) {
/* translate */
trans_1 = translate_sequence(sequence, -1, gcode, revgcode);
trans_2 = translate_sequence(sequence, -2, gcode, revgcode);
trans_3 = translate_sequence(sequence, -3, gcode, revgcode);
/* score and enter the data into the list */
score_and_enter(trans_1, matrix, -1, RepeatsAllowed, SearchType);
score_and_enter(trans_2, matrix, -2, RepeatsAllowed, SearchType);
score_and_enter(trans_3, matrix, -3, RepeatsAllowed, SearchType);
/* free the translated sequences */
free_sequence(trans_1);
free_sequence(trans_2);
free_sequence(trans_3);
}
}
/* otherwise, just use the sequence, assuming it is an AA_SEQ */
else {
/* score and enter the data into the list */
score_and_enter(sequence, matrix, 0, RepeatsAllowed, SearchType);
}
free_sequence(sequence);
records_searched++;
} /* end while there are sequences */
free_matrix(matrix);
} /* end while there are matrices */
}
static void print_stats(ofp)
FILE *ofp;
{
fprintf(ofp, "Records Searched: %d\n", records_searched);
fprintf(ofp, "\n");
fprintf(ofp, "Scores Done: %16.0f\n", Scores_Done);
fprintf(ofp, "\n");
fprintf(ofp, "Alignments Done: %16.0f\n", Alignments_Done);
fprintf(ofp, "\n");
if (DoHistogram) {
print_histogram(ofp);
}
}
/*
* main
* controls flow of program
* Parameters: argc, argv
* Error codes:
*/
int main(argc, argv)
int argc;
char *argv[];
{
FILE *ofp; /* the OutputFile file pointer */
FILE *emfp; /* the ExportMatrixFile file pointer */
FILE *fqij; /* the Qij file */
int qargc; /* args from the OP line in .cs file */
char **qargv;
char *blimps_dir; /* BLIMPS_DIR environment variable */
int i;
/* setup version info */
version_strings("BLIMPS (BLocks IMProved Searcher)",
VERSION,
"",
VERSION_DATE,
"(C) Copyright 1993-2000, Fred Hutchinson Cancer Research Center\n\n");
/* read comand line parameters */
/* NOTE:!!! Must decide if parameters or config file takes precedence */
/* will only use config file to start with, so the only arg */
/* should be the config file */
signal(SIGABRT, ABRT_signal_handler);
#ifdef MALLOC_DEBUG /* sun specific? At least not on DECs. */
malloc_debug(1); /* needed to raise the error in free(), also */
/* gives better error messages */
#endif
/* print the version info to stdout */
print_version(stdout);
ErrorLevelReport = PROGRAM_ERR_LVL; /* Most errors are suppressed */
/* check that the correct number of argments are given */
if (argc != 2) {
fprintf(stderr, "Usage: %s config_file\n", argv[0]);
exit(1);
}
/* read the configuration file, assuming it is arg 1 for now */
/* NOTE: No errors will be placed in the error file until read_config_file */
read_config_file(argv[1]);
/* See if the BLIMPS_DIR environment variable has been set */
blimps_dir = getenv("BLIMPS_DIR");
/* initialize the memory routines */
init_reclaim_space(blimps_reclaim_space);
/* initialize the list data structures used for scores, blocks, */
/* matrices, and sequences */
initialize_lists();
/* load the frequencies for converting blocks to matrices */
/* see if the frequency file has not been specified */
if (number_of_files(FREQUENCY_FILE) <= 0) {
/* get a sequence file and find out the type */
/* open the default file */
if (blimps_dir != NULL) sprintf(Buffer, "%s/docs/", blimps_dir);
else Buffer[0] = '\0';
/* When searching a block vs a DNA database, use codon frequency instead
of amino acid frequency because most of translated seq is not coding */
if( (SearchType == SEARCH_TYPE_MATRIX) &&
(get_sequence_db_seq_type() == NA_SEQ) )
{
strcat(Buffer, LOCAL_CODON_FREQUENCY_FILE);
}
else {
strcat(Buffer, LOCAL_AMINO_FREQUENCY_FILE);
}
}
else {
/* open the listed frequency file name */
strcpy(Buffer, get_current_file_name(FREQUENCY_FILE));
}
sprintf(ErrorBuffer, "Using frequencies from %s.\n", Buffer);
ErrorReport(INFO_ERR_LVL);
/* Creates global array frequency[] */
if (! load_frequencies(Buffer)) {
sprintf(ErrorBuffer, "Error loading frequencies.\n");
ErrorReport(SERIOUS_ERR_LVL);
}
/* Load the substitution probability matrix for conversion method 3 */
if (BlockToMatrixConversionMethod >= 3)
{
Qij = NULL;
if (blimps_dir != NULL) sprintf(Buffer, "%s/docs/", blimps_dir);
else Buffer[0] = '\0';
strcat(Buffer, LOCAL_QIJ_FILE);
RTot = LOCAL_QIJ_RTOT;
/* Get the arguments from the "OP alts:" line if there is one */
qargc = -1;
if (! get_option_args("alts", & qargc, & qargv)) {
sprintf(ErrorBuffer,
"Using default.qij\n");
ErrorReport(WARNING_ERR_LVL);
}
else
{
if (qargc > 0)
{
RTot = atof(qargv[0]);
if (qargc > 1) strcpy(Buffer, qargv[1]);
}
}
if ((fqij = fopen(Buffer, "r")) == NULL) {
sprintf(ErrorBuffer,
"Cannot open 'alts' file \"%s\". Exiting...\n", Buffer);
ErrorReport(FATAL_ERR_LVL);
}
Qij = load_qij(fqij);
fclose(fqij);
sprintf(ErrorBuffer,
"Using pseudo-count parameters %f and %s.\n", RTot, Buffer);
ErrorReport(INFO_ERR_LVL);
} /* end of qij file stuff */
/* initialize translation codes */
if ((0>GeneticCodeInitializer) ||
(GeneticCodeInitializer>=NUMBER_OF_GENETIC_CODES)) {
sprintf(ErrorBuffer,
"Unknown genetic code %d. Setting to Standard code (0).",
GeneticCodeInitializer);
ErrorReport(WARNING_ERR_LVL);
GeneticCodeInitializer = 0;
}
sprintf(ErrorBuffer,
"Using genetic code %d; %s.\n", GeneticCodeInitializer,
gcodes[GeneticCodeInitializer].name);
ErrorReport(INFO_ERR_LVL);
init_gcode(&gcodes[GeneticCodeInitializer], gcode, revgcode);
/* open the output file for writing */
if (OutputFile[0] != '\0') {
/* open the output file for reading */
ofp = fopen(OutputFile, "w");
if (ofp == NULL) {
sprintf(ErrorBuffer,
"Unable to open output file \"%s\" for writing, aborting.",
OutputFile);
ErrorReport(FATAL_ERR_LVL);
}
}
else {
ofp = stdout;
}
/* open the export file for writing */
if (ExportMatrixFile[0] != '\0') {
/* open the output file for reading */
emfp = fopen(ExportMatrixFile, "w");
if (emfp == NULL) {
sprintf(ErrorBuffer,
"Unable to open output file \"%s\" for writing.",
ExportMatrixFile);
ErrorReport(SERIOUS_ERR_LVL);
sprintf(ErrorBuffer,
"Not outputing the matrix output.\n");
ErrorReport(SERIOUS_ERR_LVL);
emfp = NULL;
}
}
else {
emfp = NULL;
}
/*
* read through the blocks and sequences
*/
switch (SearchType) {
case SEARCH_TYPE_BLOCK :
if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
sequence_vs_blocks(emfp);
}
else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
sequence_vs_matrices(emfp);
}
break;
case SEARCH_TYPE_MATRIX :
if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
block_vs_sequences(emfp);
}
else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
matrix_vs_sequences(emfp);
}
break;
case SEARCH_TYPE_UNKNOWN :
if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
blocks_vs_sequences(emfp); /* note plural blocks */
}
else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
matrices_vs_sequences(emfp); /* note plural matrices */
}
break;
default:
/* BIG ERROR, should never get here. Memory corrupted */
sprintf(ErrorBuffer,
"main(): SearchType variable corrupted, possible memory problems.");
ErrorReport(PROGRAM_ERR_LVL);
sprintf(ErrorBuffer,
" Should never have reached this part of the program.");
ErrorReport(PROGRAM_ERR_LVL);
sprintf(ErrorBuffer,
" The rest of the run may be invalid.");
ErrorReport(PROGRAM_ERR_LVL);
sprintf(ErrorBuffer,
" Assuming SQ vs BL search. Setting SearchType to UNKNOWN.\n");
ErrorReport(PROGRAM_ERR_LVL);
SearchType = SEARCH_TYPE_UNKNOWN;
blocks_vs_sequences(); /* note plural blocks */
break;
}
/* print out header information */
/* print the version info */
print_version(ofp);
switch (SearchType) {
case SEARCH_TYPE_BLOCK :
if (sequence != NULL) {
fprintf(ofp, "\n");
fprintf(ofp, "Probe Sequence: %s %s\n",
sequence->name, sequence->info);
fprintf(ofp, "\n");
if (sequence->type == NA_SEQ) {
fprintf(ofp, "Probe Size: %d Base Pairs\n", sequence->length);
}
else {
fprintf(ofp, "Probe Size: %d Amino Acids\n", sequence->length);
}
fprintf(ofp, "\n");
}
else {
fprintf(ofp, "\n");
fprintf(ofp, "Probe Sequence: NO SEQUENCE\n");
fprintf(ofp, "\n");
fprintf(ofp, "Probe Size: UNKNOWN\n");
fprintf(ofp, "\n");
}
fprintf(ofp, "Probe File: %s\n", get_file_name(0, SEQUENCE_FILES));
fprintf(ofp, "\n");
if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
fprintf(ofp, "Target File (s) : %s\n", get_file_name(0, BLOCK_FILES));
for(i=1; i<number_of_files(BLOCK_FILES); i++) {
fprintf(ofp, " %s\n", get_file_name(i, BLOCK_FILES));
}
}
else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
fprintf(ofp, "Target File (s) : %s\n", get_file_name(0, MATRIX_FILES));
for(i=1; i<number_of_files(MATRIX_FILES); i++) {
fprintf(ofp, " %s\n", get_file_name(i, MATRIX_FILES));
}
}
fprintf(ofp, "\n");
print_stats(ofp);
fprintf(ofp, "AC# Description");
fprintf(ofp, " Strength Score ");
fprintf(ofp, "RF AA#\n");
break;
case SEARCH_TYPE_MATRIX :
fprintf(ofp, "\n");
fprintf(ofp, "\n");
if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
fprintf(ofp, "Block File: %s\n", get_file_name(0, BLOCK_FILES));
}
else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
fprintf(ofp, "Matrix File: %s\n", get_file_name(0, MATRIX_FILES));
}
fprintf(ofp, "\n");
fprintf(ofp, "Target File (s) : %s\n", get_file_name(0, SEQUENCE_FILES));
for(i=1; i<number_of_files(SEQUENCE_FILES); i++) {
fprintf(ofp, " %s\n", get_file_name(i, SEQUENCE_FILES));
}
fprintf(ofp, "\n");
print_stats(ofp);
fprintf(ofp, "AC# Description");
fprintf(ofp, " Score ");
fprintf(ofp, "RF AA# Length\n");
break;
break;
case SEARCH_TYPE_UNKNOWN :
if (SiteSpecificScoringMatrixType == SSSM_BLOCK) {
fprintf(ofp, "Block File (s) : %s\n", get_file_name(0, BLOCK_FILES));
for(i=1; i<number_of_files(BLOCK_FILES); i++) {
fprintf(ofp, " %s\n", get_file_name(i, BLOCK_FILES));
}
}
else if (SiteSpecificScoringMatrixType == SSSM_PRECOMP_MAT) {
fprintf(ofp, "Matrix File (s) : %s\n",get_file_name(0, MATRIX_FILES));
for(i=1; i<number_of_files(MATRIX_FILES); i++) {
fprintf(ofp, " %s\n",get_file_name(i, MATRIX_FILES));
}
}
fprintf(ofp, "\n");
fprintf(ofp, "Sequence File (s) : %s\n", get_file_name(0, SEQUENCE_FILES));
for(i=1; i<number_of_files(SEQUENCE_FILES); i++) {
fprintf(ofp, " %s\n", get_file_name(i, SEQUENCE_FILES));
}
fprintf(ofp, "\n");
print_stats(ofp);
break;
default:
break;
}
/* output the data */
output_scores(NumberToReport, ofp);
/* close the output files */
fclose(ofp);
if (emfp != NULL) {
fclose(emfp);
}
/* exit with a valid code, also closes any open files that were not closed */
exit(0);
} /* end of main */
/* Change log information follows. */
/*
Changes since version 3.5:
7/22/02 Set ErrorLevelReport
Changes since version 3.3.1:
10/ 2/99 Added <string.h> & <math.h> for LINUX users.
Changes since version 3.2.5:
5/22/99 Only translate query sequence once in sequence_vs_blocks()
2/23/99 Changed sequence_vs_blocks() to use read_a_block_faster() which
ignores clusters & assumes sequence weights are in the block.
2/ 3/99 Clean up sequence_vs_blocks()
Changes since version 3.2.4:
12/12/98 Process StrandsToSearch == -1
Used default.amino.frq instead of default.codon.frq for
DNA seq vs blocks.
Changes since version 3.1.4:
5/13/98 Adjust block vs sequence search output for longer seq names.
Changes since version 3.1:
1/30/97 Changed use of default qij matrix error from SERIOUS to WARNING.
1/20/97 Fixed bug in calls to get_file_name() when multiple files
Changes since version 3.0.0:
4/22/96 Added SequenceType global variable.
4/11/96 Changed blocks_to_sequences() to call output_matrix_s(matrix,
FLOAT_OUTPUT) instead of output_matrix(matrix). This is a bad
kludge to print a matrix in floating point format by using an
"unknown" search type combination of BL with SQ. JGH
4/ 3/96 Changed to assume all conversion types >= 3 require loading a
Qij file. JGH
*/
|