00001 #include "log.h"
00002 #include "format.h"
00003 #include "fasta.h"
00004 #include "bp.h"
00005 #include <stdio.h>
00006 #include <unistd.h>
00007 #include "geneFusionsConfig.h"
00008 #include "stringUtil.h"
00009
00010 static char* getBreakPointSequence (char *tileCoordinate1, char *tileCoordinate2)
00011 {
00012 Stringa buffer;
00013 Stringa targetsFile;
00014 FILE *fp;
00015 Array targetSeqs;
00016 int i;
00017 Seq *currSeq;
00018 static Stringa sequence = NULL;
00019
00020 buffer = stringCreate (100);
00021 targetsFile = stringCreate (100);
00022 stringPrintf (targetsFile,"targets_%d.txt",getpid ());
00023 if (!(fp = fopen (string (targetsFile),"w")) ){
00024 die ("Unable to open target file: %s",string (targetsFile));
00025 }
00026 fprintf (fp,"%s\n%s",tileCoordinate1,tileCoordinate2);
00027 fclose (fp);
00028 stringPrintf (buffer,"%s %s/%s stdout -noMask -seqList=%s",
00029 BLAT_TWO_BIT_TO_FA,BLAT_DATA_DIR,BLAT_TWO_BIT_DATA_FILENAME,string (targetsFile));
00030 fasta_initFromPipe (string (buffer));
00031 targetSeqs = fasta_readAllSequences (0);
00032 fasta_deInit ();
00033 if (arrayMax (targetSeqs) != 2) {
00034 die ("Expected only two target sequences");
00035 }
00036 stringCreateClear (sequence,100);
00037 for (i = 0; i < arrayMax (targetSeqs); i++) {
00038 currSeq = arrp (targetSeqs,i,Seq);
00039 stringAppendf (sequence,"%s",currSeq->sequence);
00040 hlr_free (currSeq->name);
00041 hlr_free (currSeq->sequence);
00042 }
00043 arrayDestroy (targetSeqs);
00044 stringPrintf (buffer,"rm -rf %s",string (targetsFile));
00045 hlr_system (string (buffer),0);
00046 stringDestroy (targetsFile);
00047 stringDestroy (buffer);
00048 return string (sequence);
00049 }
00050
00051 static int sortBreakPointsByTargetAndOffset (BreakPoint *a, BreakPoint *b)
00052 {
00053 int diff;
00054 diff = strcmp (a->tileCoordinate1, b->tileCoordinate1) + strcmp(a->tileCoordinate2, b->tileCoordinate2);
00055 return diff;
00056 }
00057
00058 int main (int argc, char *argv[])
00059 {
00060 Array breakPoints;
00061 BreakPoint *currBP;
00062 int i;
00063 char *breakPointSequence;
00064
00065 bp_init ("-");
00066 breakPoints = bp_getBreakPoints ();
00067 arraySort (breakPoints,(ARRAYORDERF)sortBreakPointsByTargetAndOffset);
00068
00069 for (i = 0; i < arrayMax (breakPoints); i++) {
00070 currBP = arrp (breakPoints,i,BreakPoint);
00071 breakPointSequence = getBreakPointSequence (currBP->tileCoordinate1,currBP->tileCoordinate2);
00072 printf( ">%s|%s\n%s\n", currBP->tileCoordinate1, currBP->tileCoordinate2, breakPointSequence);
00073 warn(">%s|%s\n%s", currBP->tileCoordinate1, currBP->tileCoordinate2, subString( breakPointSequence, 10, strlen(breakPointSequence)-10));
00074 }
00075 bp_deInit();
00076 return 0;
00077 }
