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bwtformatdb.c
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#include "config.h"
#ifdef MMX
/*
BWTFormatdb.c Build index for FASTA database
This program builds index for FASTA database for use of BWTBlastn.
Copyright (C) 2006, Wong Chi Kwong.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include <stdio.h>
#include <stdlib.h>
#include "TypeNLimit.h"
#include "BWTConstruct.h"
#include "MiscUtilities.h"
#include "DNACount.h"
#include "TextConverter.h"
#include "MemManager.h"
#include "iniparser.h"
#include "HSP.h"
#include "Timing.h"
// Database and ini
dictionary *ParseInput(int argc, char** argv);
void ParseIniFile(char *iniFileName);
void ProcessIni();
void ValidateIni();
void PrintIni();
void PrintShortDesc();
void PrintHelp();
void ProcessFileName(char *outputFileName, const char *inputFileName, const char *databaseName);
// Parameters
char IniFileName[MAX_FILENAME_LEN+1];
int Confirmation;
int Pacfileonly;
// BuildTasks parameters
int ParseFASTA = TRUE;
int BuildBWT = TRUE;
int BuildSaValue = TRUE;
int BuildCachedSaIndex = TRUE;
// Memory parameters
unsigned int PoolSize = 2097152; // 2M - fixed; not configurable through ini
// Display parameters
int ShowProgress = FALSE;
// Database parameters
char FASTAFileName[MAX_FILENAME_LEN+1] = "";
char DatabaseName[MAX_FILENAME_LEN+1] = "";
char AnnotationFileName[MAX_FILENAME_LEN+1] = "*.ann";
char AmbiguityFileName[MAX_FILENAME_LEN+1] = "*.amb";
char PackedDNAFileName[MAX_FILENAME_LEN+1] = "*.pac";
char BWTCodeFileName[MAX_FILENAME_LEN+1] = "*.bwt";
char BWTOccValueFileName[MAX_FILENAME_LEN+1] = "*.fmv";
char SaValueFileName[MAX_FILENAME_LEN+1] = "*.sa";
char CachedSaIndexFileName[MAX_FILENAME_LEN+1] = "*.sai";
// Parse FASTA parameters
unsigned int FASTARandomSeed = 0;
int MaskLowerCase = FALSE;
// Build BWT parameters
unsigned int OccValueFreq = 256;
float TargetNBit = 2.5;
unsigned int InitialMaxBuildSize = 10000000;
unsigned int IncMaxBuildSize = 10000000;
// Build SA value parameters
unsigned int SaValueFreq = 8;
// Build SA index parameters
unsigned int CachedSaIndexNumOfChar = 12;
int main(int argc, char** argv) {
char c;
MMPool *mmPool;
dictionary *programInput;
double startTime;
double elapsedTime = 0, totalElapsedTime = 0;
char filename[MAX_FILENAME_LEN+1];
BWT *bwt = NULL;
unsigned int textLength = 0;
unsigned int numSeq;
BWTInc *bwtInc = NULL;
// Program input
programInput = ParseInput(argc, argv);
if (Pacfileonly)
{
ParseFASTA = TRUE;
BuildBWT = FALSE;
BuildSaValue = FALSE;
BuildCachedSaIndex = FALSE;
}
PrintShortDesc();
// Ini
if (strcmp(argv[0] + strlen(argv[0]) - 4, ".exe") == 0) {
*(argv[0] + strlen(argv[0]) - 4) = '\0';
}
sprintf(filename, "%s.ini", argv[0]);
ParseIniFile(filename);
printf("\n");
ProcessIni();
ValidateIni();
PrintIni();
if (Confirmation == TRUE) {
printf("Press Y to go or N to cancel. ");
c = (char)getchar();
while (c != 'y' && c != 'Y' && c != 'n' && c!= 'N') {
c = (char)getchar();
}
if (c == 'n' || c == 'N') {
exit(0);
}
}
startTime = setStartTime();
MMMasterInitialize(1, 0, FALSE, NULL);
mmPool = MMPoolCreate(PoolSize);
// Parse FASTA file to produce packed DNA and annotation file
if (ParseFASTA == TRUE) {
printf("Parsing FASTA file..\n");
numSeq = HSPParseFASTAToPacked(FASTAFileName, AnnotationFileName, PackedDNAFileName, AmbiguityFileName, FASTARandomSeed, MaskLowerCase);
printf("Finished. Parsed %u sequences.\n", numSeq);
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
}
// Construct BWTInc from text
if (BuildBWT == TRUE) {
printf("Building BWT..\n");
bwtInc = BWTIncConstructFromPacked(mmPool, PackedDNAFileName, ShowProgress,
TargetNBit, InitialMaxBuildSize, IncMaxBuildSize);
printf("Finished constructing BWT in %u iterations. ", bwtInc->numberOfIterationDone);
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
printf("Saving BWT..\n");
BWTSaveBwtCodeAndOcc(bwtInc->bwt, BWTCodeFileName, BWTOccValueFileName);
printf("Finished saving BWT. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
textLength = bwtInc->bwt->textLength;
BWTIncFree(mmPool, bwtInc);
}
// Load BWT
if (BuildSaValue || BuildCachedSaIndex) {
printf("Loading BWT...\n");
bwt = BWTLoad(mmPool, BWTCodeFileName, BWTOccValueFileName, NULL, NULL, NULL, NULL);
printf("Finished loading BWT. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
textLength = bwt->textLength;
}
if (BuildSaValue) {
printf("Building SA value...\n");
if (ShowProgress) {
BWTGenerateSaValue(bwt, SaValueFreq, bwt->textLength / SaValueFreq / 10);
} else {
BWTGenerateSaValue(bwt, SaValueFreq, 0);
}
BWTSaveSaValue(bwt, SaValueFileName);
printf("Finished building SA value. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
}
if (BuildCachedSaIndex) {
printf("Building cached SA index...\n");
BWTGenerateCachedSaIndex(bwt, CachedSaIndexNumOfChar, CachedSaIndexFileName);
printf("Finished building cached SA index. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
}
// Free BWT
if (BuildSaValue || BuildCachedSaIndex) {
BWTFree(mmPool, bwt);
}
// Finished all construction tasks
printf("Finished all tasks. ");
totalElapsedTime = getElapsedTime(startTime);
printf("Total elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, totalElapsedTime);
printf("\n");
MMMasterPrintReport(stdout, FALSE, FALSE, FALSE);
if (BuildSaValue) {
fprintf(stdout, "Number of char : %u\n", textLength);
fprintf(stdout, "Bit per char : %.2f\n", (float)MMMasterMaxTotalByteDispatched() * BITS_IN_BYTE / textLength);
printf("\n");
}
MMPoolFree(mmPool);
iniparser_freedict(programInput);
return 0;
}
dictionary *ParseInput(int argc, char** argv) {
dictionary *programInput;
char t1[3] = "-c"; // specify that this is a boolean type parameter
char t2[3] = "-U"; // specify that this is a boolean type parameter
char t3[3] = "-p"; // specify that this is a boolean type parameter
char *d[3];
d[0] = t1;
d[1] = t2;
d[2] = t3;
programInput = paraparser_load(argc, argv, 3, d); // 2 boolean type parameters
// Get database name
if (!iniparser_find_entry(programInput, "argument:1")) {
PrintHelp();
exit(1);
}
iniparser_copystring(programInput, "argument:1", DatabaseName, DatabaseName, MAX_FILENAME_LEN);
if (strlen(DatabaseName) + 4 > MAX_FILENAME_LEN) {
PrintHelp();
exit(1);
}
// Get FASTA file name
iniparser_copystring(programInput, "argument:2", FASTAFileName, DatabaseName, MAX_FILENAME_LEN);
if (strlen(FASTAFileName) > MAX_FILENAME_LEN) {
PrintHelp();
exit(1);
}
// Whether confirmation is needed
Confirmation = iniparser_find_entry(programInput, "parameter:-c");
MaskLowerCase = iniparser_find_entry(programInput, "parameter:-U");
Pacfileonly = iniparser_find_entry(programInput, "parameter:-p");
return programInput;
}
void ParseIniFile(char *iniFileName) {
dictionary *ini;
printf("Loading %s ..", iniFileName);
ini = iniparser_load(iniFileName, FALSE);
if (ini == NULL) {
printf("not found.\n");
return;
}
printf("done.\n");
// BuildTasks parameters
ParseFASTA = iniparser_getboolean(ini, "BuildTasks:ParseFASTA", ParseFASTA);
BuildBWT = iniparser_getboolean(ini, "BuildTasks:BuildBWT", BuildBWT);
BuildSaValue = iniparser_getboolean(ini, "BuildTasks:BuildSaValue", BuildSaValue);
BuildCachedSaIndex = iniparser_getboolean(ini, "BuildTasks:BuildCachedSaIndex", BuildCachedSaIndex);
// Display parameters
ShowProgress = iniparser_getboolean(ini, "Display:ShowProgress", ShowProgress);
// Parse FASTA parameters
FASTARandomSeed = iniparser_getint(ini, "ParseFASTA:RandomSeed", FASTARandomSeed);
if (FASTARandomSeed == 0) {
FASTARandomSeed = getRandomSeed();
}
// Build BWT parameters
OccValueFreq = iniparser_getint(ini, "BuildBWT:OccValueFreq", OccValueFreq);
TargetNBit = (float)iniparser_getdouble(ini, "BuildBWT:TargetNBit", TargetNBit);
InitialMaxBuildSize = iniparser_getint(ini, "BuildBWT:InitialMaxBuildSize", InitialMaxBuildSize);
IncMaxBuildSize = iniparser_getint(ini, "BuildBWT:IncMaxBuildSize", IncMaxBuildSize);
// Build SA value parameters
SaValueFreq = iniparser_getint(ini, "BuildSAValue:SaValueFreq", SaValueFreq);
// Build SA index parameters
CachedSaIndexNumOfChar = iniparser_getint(ini, "BuildSAIndex:CachedSaIndexNumOfChar", CachedSaIndexNumOfChar);
// Database parameters
iniparser_copystring(ini, "Database:AnnotationFileName", AnnotationFileName, AnnotationFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:AmbiguityFileName", AmbiguityFileName, AmbiguityFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:PackedDNAFileName", PackedDNAFileName, PackedDNAFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:BWTCodeFileName", BWTCodeFileName, BWTCodeFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:BWTOccValueFileName", BWTOccValueFileName, BWTOccValueFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:SaValueFileName", SaValueFileName, SaValueFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:CachedSaIndexFileName", CachedSaIndexFileName, CachedSaIndexFileName, MAX_FILENAME_LEN);
iniparser_freedict(ini);
}
void ProcessIni() {
ProcessFileName(AnnotationFileName, AnnotationFileName, DatabaseName);
ProcessFileName(AmbiguityFileName, AmbiguityFileName, DatabaseName);
ProcessFileName(PackedDNAFileName, PackedDNAFileName, DatabaseName);
ProcessFileName(BWTCodeFileName, BWTCodeFileName, DatabaseName);
ProcessFileName(BWTOccValueFileName, BWTOccValueFileName, DatabaseName);
ProcessFileName(SaValueFileName, SaValueFileName, DatabaseName);
ProcessFileName(CachedSaIndexFileName, CachedSaIndexFileName, DatabaseName);
}
void ValidateIni() {
if (!ParseFASTA && !BuildBWT && !BuildSaValue && !BuildCachedSaIndex) {
fprintf(stderr, "No action is specified!\n");
exit(1);
}
if (ParseFASTA) {
if (PackedDNAFileName[0] == '\0') {
fprintf(stderr, "Packed DNA file name is not specified!\n");
exit(1);
}
if (AnnotationFileName[0] == '\0') {
fprintf(stderr, "Annotation file name is not specified!\n");
exit(1);
}
if (AmbiguityFileName[0] == '\0') {
fprintf(stderr, "Ambiguity file name is not specified!\n");
exit(1);
}
}
if (BuildBWT) {
if (PackedDNAFileName[0] == '\0') {
fprintf(stderr, "Packed DNA file is not specified!\n");
exit(1);
}
if (BWTCodeFileName[0] == '\0') {
fprintf(stderr, "BWT code file name is not specified!\n");
exit(1);
}
if (BWTOccValueFileName[0] == '\0') {
fprintf(stderr, "BWT Occ value file name is not specified!\n");
exit(1);
}
if (TargetNBit < 2.5) {
fprintf(stderr, "Target NBit should be at least 2.5!\n");
exit(1);
}
}
if (BuildSaValue) {
if (BWTCodeFileName[0] == '\0') {
fprintf(stderr, "BWT code file is not specified!\n");
exit(1);
}
if (BWTOccValueFileName[0] == '\0') {
fprintf(stderr, "BWT Occ value file is not specified!\n");
exit(1);
}
if (SaValueFileName[0] == '\0') {
fprintf(stderr, "SA value file name is not specified!\n");
exit(1);
}
if (SaValueFreq <= 0) {
fprintf(stderr, "SA value frequency must > 0!\n");
exit(1);
}
}
if (BuildCachedSaIndex) {
if (BWTCodeFileName[0] == '\0') {
fprintf(stderr, "BWT code file is not specified!\n");
exit(1);
}
if (BWTOccValueFileName[0] == '\0') {
fprintf(stderr, "BWT Occ value file is not specified!\n");
exit(1);
}
if (CachedSaIndexFileName[0] == '\0') {
fprintf(stderr, "SA index file name is not specified!\n");
exit(1);
}
if (CachedSaIndexNumOfChar <= 0) {
fprintf(stderr, "SA index number of character must > 0!\n");
exit(1);
}
if (CachedSaIndexNumOfChar > 13) {
fprintf(stderr, "SA index number of character must <= 13!\n");
exit(1);
}
}
}
void PrintIni() {
char boolean[2];
boolean[0] = 'N';
boolean[1] = 'Y';
printf("Parse FASTA file : %c\n", boolean[ParseFASTA]);
printf("Build BWT : %c\n", boolean[BuildBWT]);
printf("Build SA value : %c\n", boolean[BuildSaValue]);
printf("Build SA index : %c\n", boolean[BuildCachedSaIndex]);
printf("\n");
printf("Show progress : %c\n", boolean[ShowProgress]);
printf("\n");
if (ParseFASTA) {
printf("Parse FASTA :\n");
printf("Mask lower case : %c\n", boolean[MaskLowerCase]);
printf("Random seed : %u\n", FASTARandomSeed);
printf("\n");
}
if (BuildBWT) {
printf("Build BWT :\n");
printf("Target N Bits : %.2f\n", TargetNBit);
printf("Occ value frequency : %u\n", OccValueFreq);
printf("Initial Max Build Size : %u Inc Max Build Size : %u\n",
InitialMaxBuildSize, IncMaxBuildSize);
printf("\n");
}
if (BuildSaValue) {
printf("Build SA value :\n");
printf("SA value frequency : %u\n", SaValueFreq);
printf("\n");
}
if (BuildCachedSaIndex) {
printf("Build SA index :\n");
printf("SA index no. of char : %u\n", CachedSaIndexNumOfChar);
printf("\n");
}
printf("Annotation file : %s\n", AnnotationFileName);
printf("Ambigurity file : %s\n", AmbiguityFileName);
printf("Packed DNA file : %s\n", PackedDNAFileName);
printf("BWT Code file : %s\n", BWTCodeFileName);
printf("BWT Occ value file : %s\n", BWTOccValueFileName);
printf("SA value file : %s\n", SaValueFileName);
printf("Cached SA index file : %s\n", CachedSaIndexFileName);
printf("\n");
}
void PrintShortDesc() {
printf("BWTFormatdb v1.0, Copyright (C) 2006, Wong Chi Kwong.\n");
printf("BWTFormatdb comes with ABSOLUTELY NO WARRENTY.\n");
printf("BWTFormatdb is free software, and you are welcome to\n");
printf("redistribute it under certain conditions.\n");
printf("For details type BWTFormatdb.\n");
printf("\n");
}
void PrintHelp() {
printf("BWTFormatdb v1.0, Copyright (C) 2006, Wong Chi Kwong.\n");
printf("\n");
printf("This program is free software; you can redistribute it and/or\n");
printf("modify it under the terms of the GNU General Public License\n");
printf("as published by the Free Software Foundation; either version 2\n");
printf("of the License, or (at your option) any later version.\n");
printf("\n");
printf("This program is distributed in the hope that it will be useful,\n");
printf("but WITHOUT ANY WARRANTY; without even the implied warranty of\n");
printf("MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n");
printf("GNU General Public License for more details.\n");
printf("\n");
printf("You should have received a copy of the GNU General Public License\n");
printf("along with this program; if not, write to the Free Software\n");
printf("Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n");
printf("\n");
printf("Syntax: BWTFormatdb <database> [FASTA file; default = <database>]\n");
printf(" [-c Confirm]\n");
printf(" [-U Mask lower case]\n");
}
void ProcessFileName(char *outputFileName, const char *inputFileName, const char *databaseName) {
char tempChar[MAX_FILENAME_LEN];
unsigned int i;
if (inputFileName == NULL) {
if (outputFileName != inputFileName) {
outputFileName[0] = '\0';
}
return;
}
if (strlen(databaseName) + strlen(inputFileName) > MAX_FILENAME_LEN) {
fprintf(stderr, "File length is too long!\n");
exit(1);
}
strncpy(tempChar, inputFileName, MAX_FILENAME_LEN);
// locate the *
for (i=0; i<MAX_FILENAME_LEN; i++) {
if (tempChar[i] == '*') {
break;
}
}
if (i<MAX_FILENAME_LEN) {
tempChar[i] = '\0';
sprintf(outputFileName, "%s%s%s", tempChar, databaseName, tempChar + i + 1);
} else {
sprintf(outputFileName, "%s", tempChar);
}
}
#else
/*
BWTFormatdb.c Build index for FASTA database
This program builds index for FASTA database for use of BWTBlastn.
Copyright (C) 2006, Wong Chi Kwong.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include <stdio.h>
#include <stdlib.h>
#include "TypeNLimit.h"
#include "BWTConstruct.h"
#include "MiscUtilities.h"
#include "DNACount.h"
#include "TextConverter.h"
#include "MemManager.h"
#include "iniparser.h"
#include "HSP.h"
#include "Timing.h"
// Database and ini
dictionary *ParseInput(int argc, char** argv);
void ParseIniFile(char *iniFileName);
void ProcessIni();
void ValidateIni();
void PrintIni();
void PrintShortDesc();
void PrintHelp();
void ProcessFileName(char *outputFileName, const char *inputFileName, const char *databaseName);
// Parameters
char IniFileName[MAX_FILENAME_LEN+1];
int Confirmation;
// BuildTasks parameters
int ParseFASTA = TRUE;
int BuildBWT = TRUE;
int BuildSaValue = TRUE;
int BuildSaIndex = TRUE;
// Memory parameters
unsigned int PoolSize = 2097152; // 2M - fixed; not configurable through ini
// Display parameters
int ShowProgress = FALSE;
// Database parameters
char FASTAFileName[MAX_FILENAME_LEN+1] = "";
char DatabaseName[MAX_FILENAME_LEN+1] = "";
char AnnotationFileName[MAX_FILENAME_LEN+1] = "*.ann";
char AmbiguityFileName[MAX_FILENAME_LEN+1] = "*.amb";
char PackedDNAFileName[MAX_FILENAME_LEN+1] = "*.pac";
char BWTCodeFileName[MAX_FILENAME_LEN+1] = "*.bwt";
char BWTOccValueFileName[MAX_FILENAME_LEN+1] = "*.fmv";
char SaValueFileName[MAX_FILENAME_LEN+1] = "*.sa";
char SaIndexFileName[MAX_FILENAME_LEN+1] = "*.sai";
// Parse FASTA parameters
unsigned int FASTARandomSeed = 0;
int MaskLowerCase = FALSE;
// Build BWT parameters
unsigned int OccValueFreq = 256;
float TargetNBit = 2.5;
unsigned int InitialMaxBuildSize = 10000000;
unsigned int IncMaxBuildSize = 10000000;
// Build SA value parameters
unsigned int SaValueFreq = 8;
// Build SA index parameters
unsigned int SaIndexNumOfChar = 12;
int main(int argc, char** argv) {
char c;
MMPool *mmPool;
dictionary *programInput;
double startTime;
double elapsedTime = 0, totalElapsedTime = 0;
char filename[MAX_FILENAME_LEN+1];
BWT *bwt = NULL;
unsigned int textLength = 0;
unsigned int numSeq;
BWTInc *bwtInc = NULL;
// Program input
programInput = ParseInput(argc, argv);
PrintShortDesc();
// Ini
if (strcmp(argv[0] + strlen(argv[0]) - 4, ".exe") == 0) {
*(argv[0] + strlen(argv[0]) - 4) = '\0';
}
sprintf(filename, "%s.ini", argv[0]);
ParseIniFile(filename);
printf("\n");
ProcessIni();
ValidateIni();
PrintIni();
if (Confirmation == TRUE) {
printf("Press Y to go or N to cancel. ");
c = (char)getchar();
while (c != 'y' && c != 'Y' && c != 'n' && c!= 'N') {
c = (char)getchar();
}
if (c == 'n' || c == 'N') {
exit(0);
}
}
startTime = setStartTime();
MMMasterInitialize(1, 0, FALSE, NULL);
mmPool = MMPoolCreate(PoolSize);
// Parse FASTA file to produce packed DNA and annotation file
if (ParseFASTA == TRUE) {
printf("Parsing FASTA file..\n");
numSeq = HSPParseFASTAToPacked(FASTAFileName, AnnotationFileName, PackedDNAFileName, AmbiguityFileName, FASTARandomSeed, MaskLowerCase);
printf("Finished. Parsed %u sequences.\n", numSeq);
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
}
// Construct BWTInc from text
if (BuildBWT == TRUE) {
printf("Building BWT..\n");
bwtInc = BWTIncConstructFromPacked(mmPool, PackedDNAFileName, ShowProgress,
TargetNBit, InitialMaxBuildSize, IncMaxBuildSize);
printf("Finished constructing BWT in %u iterations. ", bwtInc->numberOfIterationDone);
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
printf("Saving BWT..\n");
BWTSaveBwtCodeAndOcc(bwtInc->bwt, BWTCodeFileName, BWTOccValueFileName);
printf("Finished saving BWT. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
textLength = bwtInc->bwt->textLength;
BWTIncFree(mmPool, bwtInc);
}
// Load BWT
if (BuildSaValue || BuildSaIndex) {
printf("Loading BWT...\n");
bwt = BWTLoad(mmPool, BWTCodeFileName, BWTOccValueFileName, NULL, NULL, NULL, NULL);
printf("Finished loading BWT. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
textLength = bwt->textLength;
}
if (BuildSaValue) {
printf("Building SA value...\n");
if (ShowProgress) {
BWTGenerateSaValue(mmPool, bwt, SaValueFreq, bwt->textLength / SaValueFreq / 10);
} else {
BWTGenerateSaValue(mmPool, bwt, SaValueFreq, 0);
}
BWTSaveSaValue(bwt, SaValueFileName);
printf("Finished building SA value. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
}
if (BuildSaIndex) {
printf("Building SA index...\n");
BWTGenerateSaRangeTable(bwt, SaIndexNumOfChar, SaIndexFileName);
printf("Finished building SA index. ");
elapsedTime = getElapsedTime(startTime) - totalElapsedTime;
printf("Elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, elapsedTime);
totalElapsedTime += elapsedTime;
printf("\n");
}
// Free BWT
if (BuildSaValue || BuildSaIndex) {
BWTFree(mmPool, bwt);
}
// Finished all construction tasks
printf("Finished all tasks. ");
totalElapsedTime = getElapsedTime(startTime);
printf("Total elapsed time = ");
printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, totalElapsedTime);
printf("\n");
MMMasterPrintReport(stdout, FALSE, FALSE, FALSE);
if (BuildSaValue) {
fprintf(stdout, "Number of char : %u\n", textLength);
fprintf(stdout, "Bit per char : %.2f\n", (float)MMMasterMaxTotalByteDispatched() * BITS_IN_BYTE / textLength);
printf("\n");
}
MMPoolFree(mmPool);
iniparser_freedict(programInput);
return 0;
}
dictionary *ParseInput(int argc, char** argv) {
dictionary *programInput;
char t1[3] = "-c"; // specify that this is a boolean type parameter
char t2[3] = "-U"; // specify that this is a boolean type parameter
char *d[2];
d[0] = t1;
d[1] = t2;
programInput = paraparser_load(argc, argv, 2, d); // 2 boolean type parameters
// Get database name
if (!iniparser_find_entry(programInput, "argument:1")) {
PrintHelp();
exit(1);
}
iniparser_copystring(programInput, "argument:1", DatabaseName, DatabaseName, MAX_FILENAME_LEN);
if (strlen(DatabaseName) + 4 > MAX_FILENAME_LEN) {
PrintHelp();
exit(1);
}
// Get FASTA file name
iniparser_copystring(programInput, "argument:2", FASTAFileName, DatabaseName, MAX_FILENAME_LEN);
if (strlen(FASTAFileName) > MAX_FILENAME_LEN) {
PrintHelp();
exit(1);
}
// Whether confirmation is needed
Confirmation = iniparser_find_entry(programInput, "parameter:-c");
MaskLowerCase = iniparser_find_entry(programInput, "parameter:-U");
return programInput;
}
void ParseIniFile(char *iniFileName) {
dictionary *ini;
printf("Loading %s ..", iniFileName);
ini = iniparser_load(iniFileName, FALSE);
if (ini == NULL) {
printf("not found.\n");
return;
}
printf("done.\n");
// BuildTasks parameters
ParseFASTA = iniparser_getboolean(ini, "BuildTasks:ParseFASTA", ParseFASTA);
BuildBWT = iniparser_getboolean(ini, "BuildTasks:BuildBWT", BuildBWT);
BuildSaValue = iniparser_getboolean(ini, "BuildTasks:BuildSaValue", BuildSaValue);
BuildSaIndex = iniparser_getboolean(ini, "BuildTasks:BuildSaIndex", BuildSaIndex);
// Display parameters
ShowProgress = iniparser_getboolean(ini, "Display:ShowProgress", ShowProgress);
// Parse FASTA parameters
FASTARandomSeed = iniparser_getint(ini, "ParseFASTA:RandomSeed", FASTARandomSeed);
if (FASTARandomSeed == 0) {
FASTARandomSeed = getRandomSeed();
}
// Build BWT parameters
OccValueFreq = iniparser_getint(ini, "BuildBWT:OccValueFreq", OccValueFreq);
TargetNBit = (float)iniparser_getdouble(ini, "BuildBWT:TargetNBit", TargetNBit);
InitialMaxBuildSize = iniparser_getint(ini, "BuildBWT:InitialMaxBuildSize", InitialMaxBuildSize);
IncMaxBuildSize = iniparser_getint(ini, "BuildBWT:IncMaxBuildSize", IncMaxBuildSize);
// Build SA value parameters
SaValueFreq = iniparser_getint(ini, "BuildSAValue:SaValueFreq", SaValueFreq);
// Build SA index parameters
SaIndexNumOfChar = iniparser_getint(ini, "BuildSAIndex:SaIndexNumOfChar", SaIndexNumOfChar);
// Database parameters
iniparser_copystring(ini, "Database:AnnotationFileName", AnnotationFileName, AnnotationFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:AmbiguityFileName", AmbiguityFileName, AmbiguityFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:PackedDNAFileName", PackedDNAFileName, PackedDNAFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:BWTCodeFileName", BWTCodeFileName, BWTCodeFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:BWTOccValueFileName", BWTOccValueFileName, BWTOccValueFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:SaValueFileName", SaValueFileName, SaValueFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:SaIndexFileName", SaIndexFileName, SaIndexFileName, MAX_FILENAME_LEN);
iniparser_freedict(ini);
}
void ProcessIni() {
ProcessFileName(AnnotationFileName, AnnotationFileName, DatabaseName);
ProcessFileName(AmbiguityFileName, AmbiguityFileName, DatabaseName);
ProcessFileName(PackedDNAFileName, PackedDNAFileName, DatabaseName);
ProcessFileName(BWTCodeFileName, BWTCodeFileName, DatabaseName);
ProcessFileName(BWTOccValueFileName, BWTOccValueFileName, DatabaseName);
ProcessFileName(SaValueFileName, SaValueFileName, DatabaseName);
ProcessFileName(SaIndexFileName, SaIndexFileName, DatabaseName);
}
void ValidateIni() {
if (!ParseFASTA && !BuildBWT && !BuildSaValue && !BuildSaIndex) {
fprintf(stderr, "No action is specified!\n");
exit(1);
}
if (ParseFASTA) {
if (PackedDNAFileName[0] == '\0') {
fprintf(stderr, "Packed DNA file name is not specified!\n");
exit(1);
}
if (AnnotationFileName[0] == '\0') {
fprintf(stderr, "Annotation file name is not specified!\n");
exit(1);
}
if (AmbiguityFileName[0] == '\0') {
fprintf(stderr, "Ambiguity file name is not specified!\n");
exit(1);
}
}
if (BuildBWT) {
if (PackedDNAFileName[0] == '\0') {
fprintf(stderr, "Packed DNA file is not specified!\n");
exit(1);
}
if (BWTCodeFileName[0] == '\0') {
fprintf(stderr, "BWT code file name is not specified!\n");
exit(1);