int main (int argc, char *argv[]) { MrfEntry *currEntry; int mode; if (argc != 3) { usage ("%s <file.annotation> <include|exclude>",argv[0]); } intervalFind_addIntervalsToSearchSpace (argv[1],0); if (strEqual (argv[2],"include")) { mode = MODE_INCLUDE; } else if (strEqual (argv[2],"exclude")) { mode = MODE_EXCLUDE; } else { usage ("%s <file.annotation> <include|exclude>",argv[0]); } mrf_init ("-"); puts (mrf_writeHeader ()); while (currEntry = mrf_nextEntry ()) { processEntry (currEntry,mode); } mrf_deInit (); return 0; }
int main (int argc, char *argv[]) { int i,j; Array intervals; Interval *currInterval; SubInterval *currSubInterval; if (argc != 2) { usage ("%s <trackName>",argv[0]); } intervalFind_addIntervalsToSearchSpace ("-",0); intervals = intervalFind_getAllIntervals (); puts ("browser hide all"); printf ("track name=\"%s\" visibility=2\n",argv[1]); for (i = 0; i < arrayMax (intervals); i++) { currInterval = arrp (intervals,i,Interval); for (j = 0; j < arrayMax (currInterval->subIntervals); j++) { currSubInterval = arrp (currInterval->subIntervals,j,SubInterval); printf ("%s\tannotation\texon\t%d\t%d\t.\t%c\t.\tgroup%d\n", currInterval->chromosome, currSubInterval->start + 1, currSubInterval->end, currInterval->strand, i); } } 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[]) { int i,j; Array intervals; Interval *currInterval; SubInterval *currSubInterval; Stringa sizes =NULL; Stringa starts=NULL; if (argc < 2) { usage ("%s <trackName> [simple]",argv[0]); } if( (argc==3) && !strEqual( argv[2],"simple") ) { usage("%s <trackName> [simple]",argv[0]); } intervalFind_addIntervalsToSearchSpace ("-",0); intervals = intervalFind_getAllIntervals (); puts ("browser hide all"); printf ("track name=\"%s\" visibility=2\n",argv[1]); for (i = 0; i < arrayMax (intervals); i++) { currInterval = arrp (intervals,i,Interval); if( argc == 3 ) { for (j = 0; j < arrayMax (currInterval->subIntervals); j++) { currSubInterval = arrp (currInterval->subIntervals,j,SubInterval); printf ("%s\t%d\t%d\t%s_%d\t900\t%c\t%d\t%d\t.\t1\t%d\t0\n", currInterval->chromosome,currSubInterval->start,currSubInterval->end,currInterval->name,j+1,currInterval->strand, currSubInterval->start, currSubInterval->end, currSubInterval->end - currSubInterval->start ); } } else { stringCreateClear( starts, 10); stringCreateClear( sizes, 10); for( j = 0; j < arrayMax (currInterval->subIntervals); j++) { currSubInterval = arrp (currInterval->subIntervals,j,SubInterval); stringAppendf( sizes, "%d", currSubInterval->end - currSubInterval->start ); stringAppendf( starts, "%d", currSubInterval->start - currInterval->start ); if( j<arrayMax( currInterval->subIntervals) ) { stringAppendf( sizes, "," ); stringAppendf(starts, "," ); } } printf ("%s\t%d\t%d\t%s\t900\t%c\t%d\t%d\t.\t%d\t%s\t%s\n", currInterval->chromosome,currInterval->start,currInterval->end, currInterval->name,currInterval->strand, currInterval->start, currInterval->end, currInterval->subIntervalCount, string(sizes), string(starts) ); } } return 0; }
/** * \file bgrQuantifier <annotation.interval>. * \pre: it requires a BedGraph file from STDIN normalized by the number of mapped nucleotides */ int main( int argc, char* argv[] ) { Array bgrs; Array intervals; Array entries; int i, j, length; double value; if( argc < 2 ) { usage("%s <annotation.interval>\n%s requires a BedGraph from STDIN", argv[0], argv[0]); } bgrs = arrayCreate( 1000, BedGraph ); bgrParser_initFromFile ( "-" ); bgrs = bgrParser_getAllEntries (); bgrParser_deInit(); arraySort( bgrs, (ARRAYORDERF) bgrParser_sort ); intervalFind_addIntervalsToSearchSpace ( argv[1], 0 ); intervals = intervalFind_getAllIntervals (); for( i=0; i<arrayMax(intervals); i++ ) { Interval *currInterval = arrp( intervals, i, Interval ); length = currInterval->end - currInterval->start; entries = bgrParser_getValuesForRegion( bgrs, currInterval->chromosome, currInterval->start, currInterval->end); value = 0.0; for( j=0; j<arrayMax( entries ); j++) value += arru( entries, j, double ); printf("%s\t%s:%d-%d\t%f\n", currInterval->name, currInterval->chromosome, currInterval->start+1, currInterval->end, value /= length / 1000.0 ); arrayDestroy( entries ); } arrayDestroy( intervals ); return 0; }
int main (int argc, char *argv[]) { Array intervals; Interval *currInterval; SubInterval *currSubInterval; int refLength,altLength,offset; int h,i,j; Stringa buffer; Array geneTranscriptEntries; Texta geneTranscriptIds; Array alterations; Alteration *currAlteration,*nextAlteration; int numTranscripts; Stringa transcripts; VcfEntry *currVcfEntry; int position; Texta alternateAlleles; int flag1,flag2; VcfGenotype *currVcfGenotype; if (argc != 3) { usage ("%s <annotation.interval> <nameFeature>",argv[0]); } intervalFind_addIntervalsToSearchSpace (argv[1],0); geneTranscriptEntries = util_getGeneTranscriptEntries (intervalFind_getAllIntervals ()); buffer = stringCreate (100); transcripts = stringCreate (100); alterations = arrayCreate (100,Alteration); vcf_init ("-"); stringPrintf (buffer,"##INFO=<ID=VA,Number=.,Type=String,Description=\"Variant Annotation, %s, %s\">",argv[1],argv[2]); vcf_addComment (string (buffer)); puts (vcf_writeMetaData ()); puts (vcf_writeColumnHeaders ()); while (currVcfEntry = vcf_nextEntry ()) { if (vcf_isInvalidEntry (currVcfEntry)) { continue; } flag1 = 0; flag2 = 0; position = currVcfEntry->position - 1; // make zero-based alternateAlleles = vcf_getAlternateAlleles (currVcfEntry); for (h = 0; h < arrayMax (alternateAlleles); h++) { refLength = strlen (currVcfEntry->referenceAllele); altLength = strlen (textItem (alternateAlleles,h)); offset = MAX (refLength,altLength) - 1; util_clearAlterations (alterations); intervals = intervalFind_getOverlappingIntervals (currVcfEntry->chromosome,position,position + offset); for (i = 0; i < arrayMax (intervals); i++) { currInterval = arru (intervals,i,Interval*); j = 0; while (j < arrayMax (currInterval->subIntervals)) { currSubInterval = arrp (currInterval->subIntervals,j,SubInterval); if (currSubInterval->start <= position && (position + offset) < currSubInterval->end) { break; } j++; } if (j == arrayMax (currInterval->subIntervals)) { continue; } util_addAlteration (arrayp (alterations,arrayMax (alterations),Alteration),currInterval->name,argv[2],currInterval,position,0); } if (arrayMax (alterations) == 0) { continue; } arraySort (alterations,(ARRAYORDERF)util_sortAlterationsByGeneIdAndType); stringClear (buffer); i = 0; while (i < arrayMax (alterations)) { currAlteration = arrp (alterations,i,Alteration); stringAppendf (buffer,"%s%d:%s:%s:%c:%s",stringLen (buffer) == 0 ? "" : "|",h + 1,currAlteration->geneName,currAlteration->geneId,currAlteration->strand,currAlteration->type); stringClear (transcripts); stringAppendf (transcripts,"%s:%s:%d_%d",currAlteration->transcriptName,currAlteration->transcriptId,currAlteration->transcriptLength,currAlteration->relativePosition); numTranscripts = 1; j = i + 1; while (j < arrayMax (alterations)) { nextAlteration = arrp (alterations,j,Alteration); if (strEqual (currAlteration->geneId,nextAlteration->geneId) && strEqual (currAlteration->type,nextAlteration->type)) { stringAppendf (transcripts,":%s:%s:%d_%d",nextAlteration->transcriptName,nextAlteration->transcriptId,nextAlteration->transcriptLength,nextAlteration->relativePosition); numTranscripts++; } else { break; } j++; } i = j; geneTranscriptIds = util_getTranscriptIdsForGeneId (geneTranscriptEntries,currAlteration->geneId); stringAppendf (buffer,":%d/%d:%s",numTranscripts,arrayMax (geneTranscriptIds),string (transcripts)); } if (flag1 == 0) { printf ("%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s;VA=", currVcfEntry->chromosome,currVcfEntry->position,currVcfEntry->id, currVcfEntry->referenceAllele,currVcfEntry->alternateAllele, currVcfEntry->quality,currVcfEntry->filter,currVcfEntry->info); flag1 = 1; } printf ("%s%s",flag2 == 1 ? "," : "",string (buffer)); flag2 = 1; } if (flag1 == 1) { for (i = 0; i < arrayMax (currVcfEntry->genotypes); i++) { currVcfGenotype = arrp (currVcfEntry->genotypes,i,VcfGenotype); if (i == 0) { printf ("\t%s\t",currVcfEntry->genotypeFormat); } printf ("%s%s%s%s",currVcfGenotype->genotype, currVcfGenotype->details[0] != '\0' ? ":" : "", currVcfGenotype->details[0] != '\0' ? currVcfGenotype->details : "", i < arrayMax (currVcfEntry->genotypes) - 1 ? "\t" : ""); } puts (""); } } vcf_deInit (); 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[]) { Array intervals; Interval *currInterval; SubInterval *currSubInterval; int h,i,j; Array seqs; Seq *currSeq,testSeq; int index; Stringa buffer; Array geneTranscriptEntries; Texta geneTranscriptIds; Array alterations; Alteration *currAlteration,*nextAlteration; char *proteinSequenceBeforeIndel; char *proteinSequenceAfterIndel; int numDisabledTranscripts; Stringa disabledTranscripts; int seqLength,refLength,altLength; char *sequenceBeforeIndel = NULL; int overlapMode; int numOverlaps; int sizeIndel,indelOffset; int overlap; Array coordinates; VcfEntry *currVcfEntry; VcfGenotype *currVcfGenotype; int position; Texta alternateAlleles; int flag1,flag2; if (argc != 3) { usage ("%s <annotation.interval> <annotation.fa>",argv[0]); } intervalFind_addIntervalsToSearchSpace (argv[1],0); geneTranscriptEntries = util_getGeneTranscriptEntries (intervalFind_getAllIntervals ()); seq_init (); fasta_initFromFile (argv[2]); seqs = fasta_readAllSequences (0); fasta_deInit (); arraySort (seqs,(ARRAYORDERF)util_sortSequencesByName); buffer = stringCreate (100); disabledTranscripts = stringCreate (100); alterations = arrayCreate (100,Alteration); vcf_init ("-"); stringPrintf (buffer,"##INFO=<ID=VA,Number=.,Type=String,Description=\"Variant Annotation, %s\">",argv[1]); vcf_addComment (string (buffer)); puts (vcf_writeMetaData ()); puts (vcf_writeColumnHeaders ()); while (currVcfEntry = vcf_nextEntry ()) { if (vcf_isInvalidEntry (currVcfEntry)) { continue; } flag1 = 0; flag2 = 0; position = currVcfEntry->position - 1; // make zero-based alternateAlleles = vcf_getAlternateAlleles (currVcfEntry); for (h = 0; h < arrayMax (alternateAlleles); h++) { refLength = strlen (currVcfEntry->referenceAllele); altLength = strlen (textItem (alternateAlleles,h)); sizeIndel = abs (refLength - altLength); indelOffset = MAX (refLength,altLength) - 1; util_clearAlterations (alterations); intervals = intervalFind_getOverlappingIntervals (currVcfEntry->chromosome,position,position + indelOffset); for (i = 0; i < arrayMax (intervals); i++) { currInterval = arru (intervals,i,Interval*); overlapMode = OVERLAP_NONE; numOverlaps = 0; for (j = 0; j < arrayMax (currInterval->subIntervals); j++) { currSubInterval = arrp (currInterval->subIntervals,j,SubInterval); overlap = rangeIntersection (position,position + indelOffset,currSubInterval->start,currSubInterval->end); if (currSubInterval->start <= position && (position + indelOffset) < currSubInterval->end) { overlapMode = OVERLAP_FULLY_CONTAINED; numOverlaps++; } else if (j == 0 && overlap > 0 && position < currSubInterval->start) { overlapMode = OVERLAP_START; numOverlaps++; } else if (j == (arrayMax (currInterval->subIntervals) - 1) && overlap > 0 && (position + indelOffset) >= currSubInterval->end) { overlapMode = OVERLAP_END; numOverlaps++; } else if (overlap > 0 && overlap <= indelOffset) { overlapMode = OVERLAP_SPLICE; numOverlaps++; } } if (overlapMode == OVERLAP_NONE) { continue; } currAlteration = arrayp (alterations,arrayMax (alterations),Alteration); if (numOverlaps > 1) { util_addAlteration (currAlteration,currInterval->name,"multiExonHit",currInterval,position,0); continue; } else if (numOverlaps == 1 && overlapMode == OVERLAP_SPLICE) { util_addAlteration (currAlteration,currInterval->name,"spliceOverlap",currInterval,position,0); continue; } else if (numOverlaps == 1 && overlapMode == OVERLAP_START) { util_addAlteration (currAlteration,currInterval->name,"startOverlap",currInterval,position,0); continue; } else if (numOverlaps == 1 && overlapMode == OVERLAP_END) { util_addAlteration (currAlteration,currInterval->name,"endOverlap",currInterval,position,0); continue; } else if (numOverlaps == 1 && overlapMode == OVERLAP_FULLY_CONTAINED && altLength > refLength) { if ((sizeIndel % 3) == 0) { util_addAlteration (currAlteration,currInterval->name,"insertionNFS",currInterval,position,0); } else { util_addAlteration (currAlteration,currInterval->name,"insertionFS",currInterval,position,0); } } else if (numOverlaps == 1 && overlapMode == OVERLAP_FULLY_CONTAINED && altLength < refLength) { if ((sizeIndel % 3) == 0) { util_addAlteration (currAlteration,currInterval->name,"deletionNFS",currInterval,position,0); } else { util_addAlteration (currAlteration,currInterval->name,"deletionFS",currInterval,position,0); } } else if (numOverlaps == 1 && overlapMode == OVERLAP_FULLY_CONTAINED && altLength == refLength) { util_addAlteration (currAlteration,currInterval->name,"substitution",currInterval,position,0); } else { die ("Unexpected type: %d %s %s %s", currVcfEntry->position,currVcfEntry->chromosome, currVcfEntry->referenceAllele,currVcfEntry->alternateAllele); } if ((sizeIndel % 3) != 0 && altLength != refLength) { continue; } // Only run the remaining block of code if the indel is fully contained (insertion or deletion) AND does not cause a frameshift OR // if it is a substitution that is fully contained in the coding sequence stringPrintf (buffer,"%s|%s|%c|",currInterval->name,currInterval->chromosome,currInterval->strand); for (j = 0; j < arrayMax (currInterval->subIntervals); j++) { currSubInterval = arrp (currInterval->subIntervals,j,SubInterval); stringAppendf (buffer,"%d|%d%s",currSubInterval->start,currSubInterval->end,j < arrayMax (currInterval->subIntervals) - 1 ? "|" : ""); } testSeq.name = hlr_strdup (string (buffer)); if (!arrayFind (seqs,&testSeq,&index,(ARRAYORDERF)util_sortSequencesByName)) { die ("Expected to find %s in seqs",string (buffer)); } hlr_free (testSeq.name); currSeq = arrp (seqs,index,Seq); strReplace (&sequenceBeforeIndel,currSeq->sequence); seqLength = strlen (sequenceBeforeIndel); coordinates = util_getCoordinates (currInterval); // arraySort (coordinates,(ARRAYORDERF)util_sortCoordinatesByChromosomeAndTranscriptPosition); Array is already sorted by definition j = 0; stringClear (buffer); while (j < seqLength) { if (util_getGenomicCoordinate (coordinates,j,currVcfEntry->chromosome) == position) { if (altLength > refLength) { stringCat (buffer,textItem (alternateAlleles,h)); j++; continue; } else if (altLength < refLength) { stringCatChar (buffer,sequenceBeforeIndel[j]); j = j + refLength - altLength + 1; continue; } else { stringCat (buffer,textItem (alternateAlleles,h)); j = j + altLength; continue; } } stringCatChar (buffer,sequenceBeforeIndel[j]); j++; } util_destroyCoordinates (coordinates); proteinSequenceBeforeIndel = hlr_strdup (util_translate (currInterval,sequenceBeforeIndel)); proteinSequenceAfterIndel = hlr_strdup (util_translate (currInterval,string (buffer))); addSubstitution (currAlteration,proteinSequenceBeforeIndel,proteinSequenceAfterIndel,indelOffset); hlr_free (proteinSequenceBeforeIndel); hlr_free (proteinSequenceAfterIndel); } if (arrayMax (alterations) == 0) { continue; } arraySort (alterations,(ARRAYORDERF)util_sortAlterationsByGeneIdAndType); stringClear (buffer); i = 0; while (i < arrayMax (alterations)) { currAlteration = arrp (alterations,i,Alteration); stringAppendf (buffer,"%s%d:%s:%s:%c:%s",stringLen (buffer) == 0 ? "" : ",",h + 1,currAlteration->geneName,currAlteration->geneId,currAlteration->strand,currAlteration->type); stringClear (disabledTranscripts); if (currAlteration->substitution[0] != '\0') { stringAppendf (disabledTranscripts,"%s:%s:%d_%d_%s",currAlteration->transcriptName,currAlteration->transcriptId,currAlteration->transcriptLength,currAlteration->relativePosition,currAlteration->substitution); } else if (strEqual (currAlteration->type,"multiExonHit") || strEqual (currAlteration->type,"spliceOverlap") || strEqual (currAlteration->type,"startOverlap") || strEqual (currAlteration->type,"endOverlap")) { stringAppendf (disabledTranscripts,"%s:%s:%d",currAlteration->transcriptName,currAlteration->transcriptId,currAlteration->transcriptLength); } else { stringAppendf (disabledTranscripts,"%s:%s:%d_%d",currAlteration->transcriptName,currAlteration->transcriptId,currAlteration->transcriptLength,currAlteration->relativePosition); } numDisabledTranscripts = 1; j = i + 1; while (j < arrayMax (alterations)) { nextAlteration = arrp (alterations,j,Alteration); if (strEqual (currAlteration->geneId,nextAlteration->geneId) && strEqual (currAlteration->type,nextAlteration->type)) { if (nextAlteration->substitution[0] != '\0') { stringAppendf (disabledTranscripts,":%s:%s:%d_%d_%s",nextAlteration->transcriptName,nextAlteration->transcriptId,nextAlteration->transcriptLength,nextAlteration->relativePosition,nextAlteration->substitution); } else if (strEqual (nextAlteration->type,"multiExonHit") || strEqual (nextAlteration->type,"spliceOverlap") || strEqual (nextAlteration->type,"startOverlap") || strEqual (nextAlteration->type,"endOverlap")) { stringAppendf (disabledTranscripts,":%s:%s:%d",nextAlteration->transcriptName,nextAlteration->transcriptId,nextAlteration->transcriptLength); } else { stringAppendf (disabledTranscripts,":%s:%s:%d_%d",nextAlteration->transcriptName,nextAlteration->transcriptId,nextAlteration->transcriptLength,nextAlteration->relativePosition); } numDisabledTranscripts++; } else { break; } j++; } i = j; geneTranscriptIds = util_getTranscriptIdsForGeneId (geneTranscriptEntries,currAlteration->geneId); stringAppendf (buffer,":%d/%d:%s",numDisabledTranscripts,arrayMax (geneTranscriptIds),string (disabledTranscripts)); } if (flag1 == 0) { printf ("%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s;VA=", currVcfEntry->chromosome,currVcfEntry->position,currVcfEntry->id, currVcfEntry->referenceAllele,currVcfEntry->alternateAllele, currVcfEntry->quality,currVcfEntry->filter,currVcfEntry->info); flag1 = 1; } printf ("%s%s",flag2 == 1 ? "," : "",string (buffer)); flag2 = 1; } if (flag1 == 1) { for (i = 0; i < arrayMax (currVcfEntry->genotypes); i++) { currVcfGenotype = arrp (currVcfEntry->genotypes,i,VcfGenotype); if (i == 0) { printf ("\t%s\t",currVcfEntry->genotypeFormat); } printf ("%s%s%s%s",currVcfGenotype->genotype, currVcfGenotype->details[0] != '\0' ? ":" : "", currVcfGenotype->details[0] != '\0' ? currVcfGenotype->details : "", i < arrayMax (currVcfEntry->genotypes) - 1 ? "\t" : ""); } puts (""); } } vcf_deInit (); return 0; }