int main (int argc, char *argv[])
{
GfrEntry *currGE;
int i,j,k,l, h,index;
Stringa buffer,cmd,fnSequencesToAlign;
FILE *fp;
FILE *fp1;
FILE *fp2;
FILE *freads1;
FILE *freads2;
Array gfrEntries;
BowtieQuery *currBQ,testBQ;
BowtieEntry *currBE;
Texta seqNames;
int readSize1, readSize2, minReadSize;
Array bowtieQueries;
char transcriptNumber;
int isHomologous,homologousCount;
int count;
int countRemoved;
unsigned short int tooMany;
BlatQuery *blQ;
config *conf;
if ((conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL) {
die("%s:\tCannot find .fusionseqrc", argv[0]);
return EXIT_FAILURE;
}
if ( (confp_get( conf, "BLAT_TWO_BIT_TO_FA")) == NULL) {
die("%s:\tCannot find BLAT_TWO_BIT_TO_FA in the configuration file: %s", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if ( (confp_get( conf,"BLAT_DATA_DIR")) == NULL) {
die("%s:\tCannot find BLAT_DATA_DIR in the configuration file: %sc", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "TMP_DIR")==NULL ) {
die("%s:\tCannot find TMP_DIR in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "BLAT_GFSERVER")==NULL ) {
die("%s:\tCannot find BLAT_GFSERVER in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "BLAT_GFCLIENT")==NULL ) {
die("%s:\tCannot find BLAT_GFCLIENT in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "BLAT_GFSERVER_HOST")==NULL ) {
die("%s:\tCannot find BLAT_GFSERVER_HOST in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}if( confp_get( conf, "BLAT_GFSERVER_PORT")==NULL ) {
die("%s:\tCannot find BLAT_GFSERVER_PORT in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "PSEUDOGENE_DIR")==NULL ) {
die("%s:\tCannot find PSEUDOGENE_DIR in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "PSEUDOGENE_FILENAME")==NULL ) {
die("%s:\tCannot find PSEUDOGENE_FILENAME in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
cmd = stringCreate (100);
// initializing the gfServers
stringPrintf( cmd, "%s status %s %s &> /dev/null", confp_get( conf, "BLAT_GFSERVER"), confp_get( conf, "BLAT_GFSERVER_HOST"), confp_get( conf, "BLAT_GFSERVER_PORT") );
int ret = hlr_system( string(cmd), 1 );
if( ret != 0 ) { // not initialized
stringPrintf( cmd , "%s -repMatch=100000 -tileSize=12 -canStop -log=%s/gfServer_genome.log start %s %s %s/%s &", confp_get( conf, "BLAT_GFSERVER"), confp_get(conf, "TMP_DIR"),confp_get( conf, "BLAT_GFSERVER_HOST"), confp_get( conf, "BLAT_GFSERVER_PORT"), confp_get(conf, "BLAT_DATA_DIR"), confp_get(conf, "BLAT_TWO_BIT_DATA_FILENAME"));
hlr_system( string( cmd ), 0 );
long int startTime = time(0);
stringPrintf( cmd , "%s status %s %s &2> /dev/null", confp_get( conf, "BLAT_GFSERVER"), confp_get( conf, "BLAT_GFSERVER_HOST"), confp_get( conf, "BLAT_GFSERVER_PORT"));
while( hlr_system( string(cmd), 1) && (time(0)-startTime)<600 ) ;
if( hlr_system( string(cmd), 1 ) != 0 ) {
die("gfServer for %s/%s not initialized: %s %s %s", confp_get(conf, "BLAT_DATA_DIR"), confp_get(conf, "BLAT_TWO_BIT_DATA_FILENAME"), confp_get( conf, "BLAT_GFSERVER"), confp_get( conf, "BLAT_GFSERVER_HOST"), confp_get( conf, "BLAT_GFSERVER_PORT"));
return EXIT_FAILURE;
}
}
// end initialization
gfr_init ("-");
gfrEntries = gfr_parse ();
if (arrayMax (gfrEntries) == 0){
puts (gfr_writeHeader ());
gfr_deInit ();
return 0;
}
seqNames = textCreate (10000);
buffer = stringCreate (100);
fnSequencesToAlign = stringCreate (100);
count = 0;
countRemoved = 0;
stringPrintf( buffer, "%s/%s", confp_get( conf, "PSEUDOGENE_DIR"), confp_get( conf, "PSEUDOGENE_FILENAME") );
intervalFind_addIntervalsToSearchSpace (string(buffer),0);
puts (gfr_writeHeader ());
for (i = 0; i < arrayMax (gfrEntries); i++) {
currGE = arrp (gfrEntries,i,GfrEntry);
homologousCount = 0;
minReadSize=10000;
// creating two fasta files with the two genes
stringPrintf( cmd, "%s %s/%s -seq=%s -start=%d -end=%d %s/%s_transcript1.fa", confp_get(conf, "BLAT_TWO_BIT_TO_FA") , confp_get(conf, "BLAT_DATA_DIR"), confp_get(conf, "BLAT_TWO_BIT_DATA_FILENAME"), currGE->chromosomeTranscript1, currGE->startTranscript1, currGE->endTranscript1, confp_get(conf, "TMP_DIR"), currGE->id);
hlr_system( string(cmd) , 0);
stringPrintf( cmd, "%s %s/%s -seq=%s -start=%d -end=%d %s/%s_transcript2.fa", confp_get(conf, "BLAT_TWO_BIT_TO_FA"), confp_get(conf, "BLAT_DATA_DIR"), confp_get(conf, "BLAT_TWO_BIT_DATA_FILENAME"), currGE->chromosomeTranscript2, currGE->startTranscript2, currGE->endTranscript2, confp_get(conf, "TMP_DIR"), currGE->id);
hlr_system( string(cmd) , 0);
Stringa fa1 = stringCreate( 100 );
Stringa fa2 = stringCreate( 100 );
// creating the two fasta files with the reads
stringPrintf( fa1, "%s/%s_reads1.fa", confp_get(conf, "TMP_DIR"), currGE->id);
if (!(freads1 = fopen ( string(fa1) ,"w"))) {
die ("Unable to open file: %s",string (fa1));
}
// writing the reads of the first end into file
for (l = 0; l < arrayMax (currGE->readsTranscript1); l++) {
char* currRead1 = hlr_strdup( textItem (currGE->readsTranscript1,l)); // read1
readSize1 = strlen( currRead1 );
if( readSize1 == 0 ) die("Read size cannot be zero: read1[ %s ]", currRead1);
if( readSize1 < minReadSize ) minReadSize = readSize1;
fprintf( freads1, ">%d\n%s\n", l, currRead1 );
hlr_free( currRead1 );
}
fclose( freads1 );
stringPrintf( fa2, "%s/%s_reads2.fa", confp_get(conf, "TMP_DIR"), currGE->id);
if (!(freads2 = fopen ( string(fa2) ,"w"))) {
die ("Unable to open file: %s",string (fa2));
}
// writing the reads of the second end into file
for (l = 0; l < arrayMax (currGE->readsTranscript2); l++) {
char* currRead2 = hlr_strdup( textItem (currGE->readsTranscript2,l)); // read2
readSize2 = strlen( currRead2 );
if( readSize2 == 0 ) die("Read size cannot be zero: read2[ %s ]", currRead2);
if( readSize2 < minReadSize ) minReadSize = readSize2;
fprintf( freads2, ">%d\n%s\n", l, currRead2 );
hlr_free( currRead2 );
}
fclose( freads2 );
// collapse the reads 2 ## requires the FASTX package
stringPrintf( cmd, "%s -i %s/%s_reads2.fa -o %s/%s_reads2.collapsed.fa", confp_get(conf, "FASTX_COLLAPSER"), confp_get(conf, "TMP_DIR"), currGE->id, confp_get(conf, "TMP_DIR"), currGE->id );
hlr_system (string (cmd),0);
//blat of reads2 against the first transcript
stringPrintf( cmd, "%s -t=dna -out=psl -fine -tileSize=15 %s/%s_transcript1.fa %s/%s_reads2.collapsed.fa stdout",confp_get(conf, "BLAT_BLAT"), confp_get(conf, "TMP_DIR"), currGE->id, confp_get(conf, "TMP_DIR"), currGE->id );
// reading the results of blast from Pipe
blatParser_initFromPipe( string(cmd) );
while( blQ = blatParser_nextQuery() ) {
int nucleotideOverlap = getNucleotideOverlap ( blQ );
if ( nucleotideOverlap > ( ((double)readSize2)* atof(confp_get(conf,"MAX_OVERLAP_ALLOWED"))) ) {
char* value = strchr(blQ->qName,'-');
homologousCount+=atoi(value+1);
}
}
blatParser_deInit();
// collapse the reads 1 ## requires the FASTX package on the path
stringPrintf( cmd, "%s -i %s/%s_reads1.fa -o %s/%s_reads1.collapsed.fa", confp_get(conf, "FASTX_COLLAPSER"), confp_get(conf, "TMP_DIR"), currGE->id, confp_get(conf, "TMP_DIR"), currGE->id );
hlr_system (string (cmd),0);
//blat of reads1 against the second transcript
stringPrintf( cmd, "%s -t=dna -out=psl -fine -tileSize=15 %s/%s_transcript2.fa %s/%s_reads1.collapsed.fa stdout",confp_get(conf, "BLAT_BLAT"), confp_get(conf, "TMP_DIR"), currGE->id, confp_get(conf, "TMP_DIR"), currGE->id );
blatParser_initFromPipe( string(cmd) );
while( blQ = blatParser_nextQuery() ) {
int nucleotideOverlap = getNucleotideOverlap ( blQ );
if ( nucleotideOverlap > ( ((double)readSize1)* atof(confp_get(conf,"MAX_OVERLAP_ALLOWED"))) ) {
char* value = strchr(blQ->qName,'-');
homologousCount+=atoi(value+1);
}
}
blatParser_deInit();
stringPrintf (cmd,"cd %s;rm -rf %s_reads?.fa %s_reads?.collapsed.fa %s_transcript?.fa", confp_get(conf, "TMP_DIR"), currGE->id,currGE->id,currGE->id);
hlr_system( string(cmd) , 0);
if (((double)homologousCount / (double)arrayMax(currGE->readsTranscript1)) <= atof(confp_get(conf, "MAX_FRACTION_HOMOLOGOUS")) ) {
homologousCount = 0;
// there is no homology between the two genes, but what about the rest of the genome
writeFasta( currGE, &minReadSize, confp_get(conf, "TMP_DIR") );
stringPrintf(cmd, "cd %s; %s %s %s / -t=dna -q=dna -minScore=%d -out=psl %s_reads.fa %s.smallhomology.psl &>/dev/null", confp_get(conf, "TMP_DIR"), confp_get( conf, "BLAT_GFCLIENT"), confp_get( conf, "BLAT_GFSERVER_HOST"), confp_get( conf, "BLAT_GFSERVER_PORT"), minReadSize - (int)(0.1 * minReadSize) > 20 ? minReadSize - (int) (0.1 * minReadSize) : 20 , currGE->id, currGE->id);
int attempts=0;
ret = hlr_system( string(cmd), 1 );
while( hlr_system( string(cmd), 1 ) && attempts<5000 ) attempts++;
if( attempts == 5000 ) {
die("Cannot map the reads %s", string( cmd ));
return EXIT_FAILURE;
}
// reading the results of blast from File
stringPrintf(cmd, "%s/%s.smallhomology.psl", confp_get( conf, "TMP_DIR"), currGE->id);
blatParser_initFromFile( string(cmd) );
tooMany = 1;
while( blQ = blatParser_nextQuery() ) {
tooMany = 0;
checkPseudogeneOverlap( blQ );
if( arrayMax( blQ->entries ) > 1 ) {
homologousCount+= arrayMax( blQ->entries ) - 1;
char* value = strchr( blQ->qName,'/' );
if( value ) *value = '\0'; else die("Not a valid index in the blat query name:\t%s", blQ->qName );
int indexOfInter = atoi( blQ->qName ); // the following three lines should removed the read if writing the GFR entry
GfrInterRead *currGIR = arrp( currGE->interReads, indexOfInter, GfrInterRead );
currGIR->flag = 1;
}
}
blatParser_deInit();
if ( tooMany == 1 || ( ( (double) homologousCount / (double) ( arrayMax(currGE->readsTranscript1) + arrayMax(currGE->readsTranscript2) ) ) > atof(confp_get(conf, "MAX_FRACTION_HOMOLOGOUS")) ) ) {
countRemoved++;
stringPrintf (cmd,"cd %s; rm -rf %s_reads*.fa %s_reads?.collapsed.fa %s_transcript?.fa %s.smallhomology.psl", confp_get(conf, "TMP_DIR"), currGE->id,currGE->id,currGE->id,currGE->id);
hlr_system( string(cmd), 1 );
continue;
}
// writing the gfrEntry, if everthing else didn't stop
if( homologousCount > 0 ) updateStats( currGE );
puts (gfr_writeGfrEntry (currGE));
count++;
// removing temporary files
stringPrintf (cmd,"cd %s;rm -rf %s_reads*.fa %s_reads?.collapsed.fa %s_transcript?.fa %s.smallhomology.psl", confp_get(conf, "TMP_DIR"), currGE->id,currGE->id,currGE->id,currGE->id);
hlr_system( string(cmd) , 1);
} else {
countRemoved++;
}
}
gfr_deInit ();
stringDestroy (fnSequencesToAlign);
stringDestroy (cmd);
stringDestroy (buffer);
warn ("%s_numRemoved: %d",argv[0],countRemoved);
warn ("%s_numGfrEntries: %d",argv[0],count);
confp_close(conf);
return EXIT_SUCCESS;
}
int main (int argc, char *argv[])
{
GfrEntry *currGE;
int count;
int countRemoved;
int mitochondrialCount;
unsigned int minReadSize;
int i;
Stringa cmd;
BlatQuery *blQ=NULL;
config *conf = NULL; /**< Pointer to configuration file .fusionseqrc */
if ((conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL) {
die("%s:\tCannot find .fusionseqrc: %s", argv[0], getenv("FUSIONSEQ_CONFPATH"));
return EXIT_FAILURE;
}
if( confp_get( conf,"MAX_OVERLAP_ALLOWED")==NULL ) {
die("%s:\tCannot find MAX_OVERLAP_ALLOWED in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf,"MAX_FRACTION_HOMOLOGOUS")==NULL ) {
die("%s:\tCannot find MAX_FRACTION_HOMOLOGOUS in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "MITOCHONDRIAL_DIR")==NULL ) {
die("%s:\tCannot find MITOCHONDRIAL_DIR in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "MITOCHONDRIAL_FILENAME")==NULL ) {
die("%s:\tCannot find MITOCHONDRIAL_FILENAME in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "TMP_DIR")==NULL ) {
die("%s:\tCannot find TMP_DIR in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "BLAT_GFSERVER")==NULL ) {
die("%s:\tCannot find BLAT_GFSERVER in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "BLAT_GFCLIENT")==NULL ) {
die("%s:\tCannot find BLAT_GFCLIENT in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
if( confp_get( conf, "BLAT_GFSERVER_HOST")==NULL ) {
die("%s:\tCannot find BLAT_GFSERVER_HOST in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}if( confp_get( conf, "BLAT_GFSERVER_PORT")==NULL ) {
die("%s:\tCannot find BLAT_GFSERVER_PORT in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") );
return EXIT_FAILURE;
}
count = 0;
countRemoved = 0;
cmd = stringCreate (100);
// initializing the gfServers
stringPrintf( cmd, "%s status %s %d &> /dev/null", confp_get( conf, "BLAT_GFSERVER"), confp_get( conf, "BLAT_GFSERVER_HOST"), atoi(confp_get( conf, "BLAT_GFSERVER_PORT")) + 2);
int ret = hlr_system( string(cmd), 1 );
if( ret != 0 ) { // not initialized
stringPrintf( cmd , "%s -repMatch=100000 -tileSize=12 -canStop -log=%s/gfServer_mitochondrial.log start %s %d %s/%s &", confp_get( conf, "BLAT_GFSERVER"), confp_get( conf, "TMP_DIR"), confp_get( conf, "BLAT_GFSERVER_HOST"), atoi(confp_get( conf, "BLAT_GFSERVER_PORT")) + 2, confp_get( conf, "MITOCHONDRIAL_DIR"), confp_get( conf,"MITOCHONDRIAL_FILENAME"));
hlr_system( string( cmd ), 0 );
long int startTime = time(0);
stringPrintf( cmd , "%s status %s %d &> /dev/null", confp_get( conf, "BLAT_GFSERVER"), confp_get( conf, "BLAT_GFSERVER_HOST"), atoi(confp_get( conf, "BLAT_GFSERVER_PORT")) + 2);
while( hlr_system( string(cmd), 1) && (time(0)-startTime)<600 ) ;
if( hlr_system( string(cmd), 1 ) != 0 ) {
die("gfServer for %s/%s not initialized: %s %s %s", confp_get( conf, "MITOCHONDRIAL_DIR"), confp_get( conf, "MITOCHONDRIAL_FILENAME"), confp_get( conf, "BLAT_GFSERVER"), confp_get( conf, "BLAT_GFSERVER_HOST"), confp_get( conf, "BLAT_GFSERVER_PORT"));
return EXIT_FAILURE;
}
}
gfr_init ("-");
puts (gfr_writeHeader ());
while (currGE = gfr_nextEntry ()) {
if (strEqual(currGE->chromosomeTranscript1, "chrM") ||
strEqual(currGE->chromosomeTranscript2, "chrM")) {
countRemoved++;
continue;
} else {
mitochondrialCount = 0;
minReadSize=1000;
writeFasta( currGE, &minReadSize, confp_get( conf, "TMP_DIR") ); // in util.c
stringPrintf(cmd, "cd %s;%s %s %d / -t=dna -q=dna -minScore=%d -out=psl %s_reads.fa %s.mito.psl &>/dev/null", confp_get( conf, "TMP_DIR"), confp_get( conf, "BLAT_GFCLIENT"), confp_get( conf, "BLAT_GFSERVER_HOST"), atoi(confp_get( conf, "BLAT_GFSERVER_PORT")) + 2, minReadSize - 5 > 20 ? minReadSize - 5 : 20 , currGE->id, currGE->id);
int attempts=0;
ret = hlr_system( string(cmd), 1 );
while( hlr_system( string(cmd), 1 ) && attempts<5000 ) attempts++;
if( attempts == 5000 ) {
die("Cannot map the reads %s", string( cmd ));
return EXIT_FAILURE;
}
// reading the results of blast from File
stringPrintf(cmd, "%s/%s.mito.psl", confp_get( conf, "TMP_DIR"), currGE->id);
blatParser_initFromFile( string(cmd) );
while( blQ = blatParser_nextQuery() ) {
//warn("iter %d\tquery %s", iter, blQ->qName );iter++;
int nucleotideOverlap = getNucleotideOverlap ( blQ );
if (nucleotideOverlap > (((double) minReadSize) * strtod(confp_get( conf, "MAX_OVERLAP_ALLOWED"), NULL))) {
char* value = strchr( blQ->qName,'/' );
if( value ) *value = '\0'; else die("Not a valid index in the blat query name:\t%s", blQ->qName );
int indexOfInter = atoi( blQ->qName ); // the following three lines should removed the read if writing the GFR entry
GfrInterRead *currGIR = arrp( currGE->interReads, indexOfInter, GfrInterRead );
currGIR->flag = 1;
mitochondrialCount++;
}
}
blatParser_deInit();
if ( ( (double) mitochondrialCount / (double) ( arrayMax(currGE->readsTranscript1) + arrayMax(currGE->readsTranscript2) ) ) <= strtod(confp_get( conf, "MAX_FRACTION_HOMOLOGOUS"), NULL)) {
if( mitochondrialCount > 0 ) updateStats( currGE );
// writing the gfrEntry
puts (gfr_writeGfrEntry (currGE));
count++;
} else {
countRemoved++;
}
// removing temporary files
stringPrintf (cmd,"rm -rf %s/%s_reads.fa %s/%s.mito.psl", confp_get( conf, "TMP_DIR"), currGE->id, confp_get( conf, "TMP_DIR"), currGE->id );
hlr_system( string(cmd) , 1);
}
}
gfr_deInit ();
stringDestroy( cmd );
warn ("%s_numRemoved: %d",argv[0],countRemoved);
warn ("%s_numGfrEntries: %d",argv[0],count);
confp_close(conf);
return 0;
}
int main(int argc, char * const argv[]) {
GArgs args(argc, argv, "hFCq:r:o:");
int e;
if ((e=args.isError())>0)
GError("%s\nInvalid argument: %s\n", USAGE, argv[e]);
if (args.getOpt('h')!=NULL){
GMessage("%s\n", USAGE);
exit(1);
}
args.startNonOpt();
GStr fadb(args.nextNonOpt());
if (fadb.is_empty()) GError("%s Error: multi-fasta file expected!\n",USAGE);
GStr fname(fadb);
fname.append(".fai");
bool createLocal=(args.getOpt('F')!=NULL);
const char* idxname=(createLocal)? NULL : fname.chars();
GFastaIndex faidx(fadb.chars(), idxname);
//also tried to load the index if exists in the current directory
GStr fnamecwd(fname); //name in current directory (without path)
int ip=-1;
if ((ip=fnamecwd.rindex(CHPATHSEP))>=0) {
fnamecwd.cut(0,ip+1);
}
if (!createLocal) { //look for existing indexes to load
//try the same directory as the fasta file first
if (!faidx.hasIndex() and fileExists(fnamecwd.chars())>1) { //try current working directory next
faidx.loadIndex(fnamecwd.chars());
}
if (!faidx.hasIndex()) {//could not load any index data
//try to create it in the same directory as the fasta file
GMessage("No fasta index found. Rebuilding..\n");
faidx.buildIndex();
if (faidx.getCount()==0) GError("Error: no fasta records to be indexed!\n");
GMessage("Fasta index rebuilt.\n");
//check if we can create a file there
FILE* fcreate=fopen(fname.chars(), "w");
if (fcreate==NULL)
GMessage("Warning: cannot create fasta index %s! (permissions?)\n", fname.chars());
else {
fclose(fcreate);
if (faidx.storeIndex(fname.chars())<faidx.getCount())
GMessage("Warning: error writing the index file %s!\n",fname.chars());
} //creating index file in the same directory as fasta file
}//trying to create the index file
}
if (createLocal || !faidx.hasIndex()) {
//simply rebuild the index in the current directory and use it:
//remove directories in path, if any
if (faidx.getCount()==0) {
faidx.buildIndex();
if (faidx.getCount()==0) GError("Error: no fasta records to be indexed!\n");
}
if (faidx.storeIndex(fnamecwd.chars())<faidx.getCount())
GMessage("Warning: error writing the index file %s!\n",fnamecwd.chars());
}
GStr qry(args.getOpt('q'));
if (qry.is_empty()) exit(0);
GFastaRec* farec=faidx.getRecord(qry.chars());
if (farec==NULL) {
GMessage("Error: couldn't find fasta record for '%s'!\n",qry.chars());
exit(1);
}
GFaSeqGet faseq(fadb.chars(),farec->seqlen, farec->fpos, farec->line_len, farec->line_blen);
//TODO: read these from -r option
uint qstart=0;
uint qend=0; //farec->seqlen
bool revCompl=(args.getOpt('C')!=NULL);
char* s=args.getOpt('r');
if (s!=NULL) {
char *p=s;
while (isdigit(*p)) p++;
if (*p=='-') {
sscanf(s,"%u-%u",&qstart, &qend);
if (qstart==0 || qend==0)
GError("Error parsing sequence range: %s\n",s);
}
else if (*p==':') {
int qlen=0;
sscanf(s,"%u:%d", &qstart, &qlen);
if (qstart==0 || qlen==0)
GError("Error parsing sequence range: %s\n",s);
qend=qstart+qlen-1;
}
else if (*p=='.') {
sscanf(s,"%u..%u",&qstart, &qend);
if (qstart==0 || qend==0)
GError("Error parsing sequence range: %s\n",s);
}
}
if (qstart==0) qstart=1;
if (qend==0) qend=farec->seqlen;
// call faseq.loadall() here if multiple ranges are to be extracted all
// over this genomic sequence
char* subseq=faseq.copyRange(qstart, qend, revCompl, true);
FILE* f_out=NULL;
openfwrite(f_out, args, 'o');
if (f_out==NULL) f_out=stdout;
writeFasta(f_out, qry.chars(), NULL, subseq, 70, qend-qstart+1);
GFREE(subseq);
}
