int main (int argc, char *argv[]) { GfrEntry *currGE; int count; int countRemoved; if (argc != 2) { usage ("%s <string>",argv[0]); } count = 0; countRemoved = 0; gfr_init ("-"); puts (gfr_writeHeader ()); while (currGE = gfr_nextEntry ()) { if (currGE->descriptionTranscript1 == NULL || currGE->descriptionTranscript2 == NULL) { die ("Transcript description is missing"); } if (strCaseStr (currGE->descriptionTranscript1,argv[1]) || strCaseStr (currGE->descriptionTranscript2,argv[1])) { countRemoved++; continue; } puts (gfr_writeGfrEntry (currGE)); count++; } gfr_deInit (); warn ("%s_string: %s",argv[0],argv[1]); warn ("%s_numRemoved: %d",argv[0],countRemoved); warn ("%s_numGfrEntries: %d",argv[0],count); return 0; }
int main (int argc, char *argv[]) { GfrEntry *currGE; int count; int countRemoved; int i; if (argc != 3) { usage ("%s <offsetCutoff> <minNumUniqueReads>",argv[0]); } count = 0; countRemoved = 0; int offsetCutOff = atoi (argv[1]); int minNumUniqueReads = atoi (argv[2]); gfr_init ("-"); puts (gfr_writeHeader ()); while (currGE = gfr_nextEntry ()) { Array starts = arrayCreate( 100, int); for (i = 0; i < arrayMax( currGE->interReads ); i++) { int currStart = arrp(currGE->interReads, i, GfrInterRead)->readStart1 + arrp(currGE->interReads, i, GfrInterRead)->readStart2; array(starts, arrayMax(starts), int) = currStart; } arraySort( starts, (ARRAYORDERF) arrayIntcmp ); arrayUniq( starts, NULL, (ARRAYORDERF) arrayIntcmp ) ; int numUniqeOffsets = arrayMax( starts ); arrayDestroy( starts ); if (arrayMax( currGE->readsTranscript1 ) != arrayMax( currGE->readsTranscript2 ) ) die( "The two ends have a different number of reads"); Texta reads = textCreate(arrayMax(currGE->readsTranscript1)); for (i = 0; i < arrayMax(currGE->readsTranscript1); i++) { Stringa strA = stringCreate( strlen(textItem( currGE->readsTranscript1, i) ) * 2 + 1); stringAppendf( strA, textItem( currGE->readsTranscript1,i)); stringAppendf( strA, textItem( currGE->readsTranscript2,i)); textAdd( reads, string(strA)); stringDestroy( strA ); } textUniqKeepOrder( reads ); int numRemaining = arrayMax( reads ); textDestroy ( reads ); if (numRemaining <= minNumUniqueReads || numUniqeOffsets <= offsetCutOff) { countRemoved++; continue; } puts (gfr_writeGfrEntry (currGE)); count++; } gfr_deInit (); warn("%s_PCRFilter: offset=%d minNumUniqueReads=%d", argv[0],offsetCutOff, minNumUniqueReads); warn("%s_numRemoved: %d",argv[0],countRemoved); warn("%s_numGfrEntries: %d",argv[0],count); return 0; }
int main (int argc, char *argv[]) { GfrEntry *currGE; int count; int countRemoved; int i, j; int foundEST; if (argc != 2) { usage ("%s <EST.interval>",argv[0]); } intervalFind_addIntervalsToSearchSpace( argv[1], 0); // beginFiltering count = 0; countRemoved = 0; gfr_init ("-"); puts (gfr_writeHeader ()); while (currGE = gfr_nextEntry ()) { // reading the gfr foundEST = 0; if( strEqual( currGE->fusionType, "cis" ) ) { if( ! strEqual( currGE->chromosomeTranscript1, currGE->chromosomeTranscript2 ) ) die("The two genes are not on the same chromosomes: %s - %s", currGE->chromosomeTranscript1, currGE->chromosomeTranscript2 ); int start1, end1, start2, end2; findCoordinates( currGE, &start1, &end1, &start2, &end2 ); Array intervals1 = arrayCopy( intervalFind_getOverlappingIntervals( currGE->chromosomeTranscript1, start1, end1 ) ); Array intervals2 = intervalFind_getOverlappingIntervals( currGE->chromosomeTranscript2, start2, end2 ); for( i=0; i<arrayMax( intervals1 ); i++ ) { Interval* currInterval1 = arru( intervals1, i, Interval* ); for( j=0; j<arrayMax ( intervals2 ); j++ ) { Interval* currInterval2 = arru( intervals2, j, Interval* ); if( currInterval1==currInterval2 ) { foundEST = 1; i = arrayMax( intervals1 ); j = arrayMax( intervals2 ); } } } arrayDestroy( intervals1 ); } if( foundEST ) countRemoved++; else { puts (gfr_writeGfrEntry (currGE)); count++; } } gfr_deInit (); warn ("%s_EST_data: %s",argv[0], argv[1]); warn ("%s_numRemoved: %d",argv[0], countRemoved); warn ("%s_numGfrEntries: %d",argv[0],count); return 0; }
int main (int argc, char *argv[]) { GfrEntry *currGE; int count; gfr_init ("-"); gfr_addNewColumnType (GFR_COLUMN_NAME_PAIR_COUNT); puts (gfr_writeHeader ()); count = 0; while (currGE = gfr_nextEntry ()){ obtainPairCounts (currGE); puts (gfr_writeGfrEntry (currGE)); fflush (stdout); count++; } gfr_deInit (); warn ("%s_numGfrEntries: %d",argv[0],count); return 0; }
int main (int argc, char *argv[]) { GfrEntry *currGE; Array kgTreeFams; Stringa buffer; int count; int countRemoved; config *conf; if ((conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL) return EXIT_FAILURE; buffer = stringCreate (100); stringPrintf (buffer,"%s/%s", confp_get(conf, "ANNOTATION_DIR"), confp_get(conf, "KNOWN_GENE_TREE_FAM_FILENAME")); kgTreeFams = util_readKnownGeneTreeFams (string (buffer)); arraySort (kgTreeFams,(ARRAYORDERF)sortKgTreeFamsByTranscriptName); stringDestroy (buffer); count = 0; countRemoved = 0; gfr_init ("-"); puts (gfr_writeHeader ()); while (currGE = gfr_nextEntry ()){ if (isHomologous (kgTreeFams,currGE->nameTranscript1,currGE->nameTranscript2)) { countRemoved++; continue; } puts (gfr_writeGfrEntry (currGE)); count++; } gfr_deInit (); 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; GfrInterRead *currGIR; int i; Stringa buffer; FILE *fp1,*fp2; int count; count = 0; buffer = stringCreate (100); gfr_init ("-"); puts (gfr_writeHeader ()); while (currGE = gfr_nextEntry ()) { stringPrintf (buffer,"%s_1.bed",currGE->id); fp1 = fopen (string (buffer),"w"); stringPrintf (buffer,"%s_2.bed",currGE->id); fp2 = fopen (string (buffer),"w"); if (fp1 == NULL || fp2 == NULL) { die ("Unable to open BED files"); } fprintf (fp1,"browser full knownGene\n"); fprintf (fp1,"track name=\"Inter paird-ends: %s_1\" visibility=2\n",currGE->id); fprintf (fp2,"browser full knownGene\n"); fprintf (fp2,"track name=\"Inter paird-ends: %s_2\" visibility=2\n",currGE->id); for (i = 0; i < arrayMax (currGE->interReads); i++) { currGIR = arrp (currGE->interReads,i,GfrInterRead); fprintf (fp1,"%s\t%d\t%d\n",currGE->chromosomeTranscript1,currGIR->readStart1,currGIR->readEnd1); fprintf (fp2,"%s\t%d\t%d\n",currGE->chromosomeTranscript2,currGIR->readStart2,currGIR->readEnd2); } fclose (fp1); fclose (fp2); puts (gfr_writeGfrEntry (currGE)); count++; } gfr_deInit (); stringDestroy (buffer); warn ("%s_numGfrEntries: %d",argv[0],count); return 0; }
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 *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; BLEntry *currBLE; BLEntry currQuery; FILE *fp; char *line; int count; int countRemoved; int index; WordIter w; Array blackList = arrayCreate(20, BLEntry); if (argc != 2) { usage ("%s <blackList.txt>",argv[0]); } fp = fopen( argv[1], "r" ); if( !fp ) die("Unable to open file: %s", argv[1]); // reading blacklist file LineStream ls = ls_createFromFile( argv[1] ); while( line = ls_nextLine(ls) ) { w = wordIterCreate( line, "\t", 1); currBLE = arrayp( blackList, arrayMax(blackList), BLEntry); currBLE->gene1 = hlr_strdup ( wordNext(w) ); currBLE->gene2 = hlr_strdup ( wordNext(w) ); wordIterDestroy(w); } fclose(fp); arraySort( blackList, (ARRAYORDERF) sortBlackListByName1); // beginFiltering count = 0; countRemoved = 0; gfr_init ("-"); puts (gfr_writeHeader ()); while (currGE = gfr_nextEntry ()) { // reading the gfr // creating a new query to the black list currQuery.gene1 = currGE->geneSymbolTranscript1; currQuery.gene2 = currGE->geneSymbolTranscript2; // searching against read_1/read_2 int res = arrayFind( blackList, &currQuery, &index, (ARRAYORDERF) sortBlackListByName1); if( !res ) { // not found, then searching against read_2/read_1 currQuery.gene1 = currGE->geneSymbolTranscript2; currQuery.gene2 = currGE->geneSymbolTranscript1; res = arrayFind( blackList, &currQuery, &index, (ARRAYORDERF) sortBlackListByName1 ); if( !res ) { // not found, write the instance to stdout, update the counts puts (gfr_writeGfrEntry (currGE)); count++; } else { // found: read2/read1 countRemoved++; } } else { //found: read1/read2 countRemoved++; } } gfr_deInit (); arrayDestroy( blackList ); warn ("%s_BlackListFilter: %s",argv[0], argv[1]); warn ("%s_numRemoved: %d",argv[0],countRemoved); warn ("%s_numGfrEntries: %d",argv[0],count); return 0; }
int main (int argc, char *argv[]) { GfrEntry *currGE; BLEntry *currBLE; BLEntry currQuery; FILE *fp; char *line; int count; int countRemoved; int index; WordIter w; Array blackList = arrayCreate(20, BLEntry); config *Conf; 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, "ANNOTATION_DIR")==NULL ) { die("%s:\tCannot find ANNOTATION_DIR in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") ); return EXIT_FAILURE; } if( confp_get( Conf, "BLACKLIST_FILENAME")==NULL ) { die("%s:\tCannot find BLACKLIST_FILENAME in the configuration file: %s)", argv[0], getenv("FUSIONSEQ_CONFPATH") ); return EXIT_FAILURE; } Stringa buffer=stringCreate( 100 ); stringPrintf( buffer, "%s/%s", confp_get( Conf, "ANNOTATION_DIR"), confp_get( Conf, "BLACKLIST_FILENAME") ); /* fp = fopen( string( buffer ), "r" ); if( !fp ) die("Unable to open file: %s", string(buffer)); stringDestroy( buffer ); */ // reading blacklist file LineStream ls = ls_createFromFile( string(buffer) ); while( line = ls_nextLine(ls) ) { w = wordIterCreate( line, "\t", 1); currBLE = arrayp( blackList, arrayMax(blackList), BLEntry); currBLE->gene1 = hlr_strdup ( wordNext(w) ); currBLE->gene2 = hlr_strdup ( wordNext(w) ); wordIterDestroy(w); } //fclose(fp); ls_destroy( ls ); stringDestroy( buffer ); arraySort( blackList, (ARRAYORDERF) sortBlackListByName1); // beginFiltering count = 0; countRemoved = 0; gfr_init ("-"); puts (gfr_writeHeader ()); while (currGE = gfr_nextEntry ()) { // reading the gfr if( currGE->geneSymbolTranscript1 == NULL ) { die("Gene symbols are not present in the GFR file. Please run gfrAddInfo before gfrBlackListFilter."); return EXIT_FAILURE; } // creating a new query to the black list currQuery.gene1 = currGE->geneSymbolTranscript1; currQuery.gene2 = currGE->geneSymbolTranscript2; if( strEqual( currQuery.gene1 , currQuery.gene2 ) ) { countRemoved++; continue; } // searching against read_1/read_2 int res = arrayFind( blackList, &currQuery, &index, (ARRAYORDERF) sortBlackListByName1); if( !res ) { // not found, then searching against read_2/read_1 currQuery.gene1 = currGE->geneSymbolTranscript2; currQuery.gene2 = currGE->geneSymbolTranscript1; res = arrayFind( blackList, &currQuery, &index, (ARRAYORDERF) sortBlackListByName1 ); if( !res ) { // not found, write the instance to stdout, update the counts puts (gfr_writeGfrEntry (currGE)); count++; } else { // found: read2/read1 countRemoved++; } } else { //found: read1/read2 countRemoved++; } } gfr_deInit (); arrayDestroy( blackList ); warn ("%s_BlackListFilter: %s",argv[0], confp_get( Conf, "BLACKLIST_FILENAME")); warn ("%s_numRemoved: %d",argv[0],countRemoved); warn ("%s_numGfrEntries: %d",argv[0],count); confp_close( Conf); return 0; }