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gpertea |
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#include "GArgs.h" |
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#include "GStr.h" |
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#include "gtf_tracking.h" |
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GList<GSeqData> ref_data(true,true,true); //list of reference mRNAs and loci data for each genomic seq |
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//each locus will keep track of any superloci which includes it, formed during the analysis |
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int main(int argc, char * const argv[]) { |
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GArgs args(argc, argv, "FCRPq:r:o:"); |
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GList<GSeqData>* rnas; |
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args.startNonOpt(); |
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GStr gtfile(args.nextNonOpt()); |
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if (gtfile.is_empty()) GError("Usage: test_load [-R] [{-P|-o <outgff>}] <gff_input>\nNo input GFF file given!\n"); |
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gtf_tracking_verbose=true; |
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FILE* RNA_file=fopen(gtfile.chars(), "rb"); |
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if (RNA_file==NULL) GError("Error opening file %s!\n",gtfile.chars()); |
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//read_transcripts(mRNA_file, rnas, true); |
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bool load_as_ref=(args.getOpt('R')!=NULL); |
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if (load_as_ref) { |
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rnas=&ref_data; |
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read_mRNAs(RNA_file, *rnas, NULL, true, -1, gtfile.chars()); |
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} |
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else { |
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rnas=new GList<GSeqData>(true,true,true); |
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read_mRNAs(RNA_file, *rnas, &ref_data, true, 0, gtfile.chars()); |
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} |
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fclose(RNA_file); |
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int fcount=0; |
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int rcount=0; |
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int ucount=0; |
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for (int i=0;i<rnas->Count();i++) { |
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fcount+=rnas->Get(i)->mrnas_f.Count(); |
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rcount+=rnas->Get(i)->mrnas_r.Count(); |
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ucount+=rnas->Get(i)->umrnas.Count(); |
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} |
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int mtotal=fcount+rcount+ucount; |
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GStr oname(args.getOpt('o')); |
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FILE* fout=NULL; |
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if (!oname.is_empty()) fout=fopen(oname.chars(), "w"); |
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else if (args.getOpt('P')) fout=stdout; |
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GMessage("Totals:\n%6d on forward strand\n" |
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"%6d on reverse strand\n%6d unknown strand\n" |
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"--------------------------\n%6d total\n", |
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fcount, rcount, ucount, mtotal); |
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if (fout) { |
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for (int i=0;i<rnas->Count();i++) { |
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for (int k=0;k<rnas->Get(i)->mrnas_f.Count();k++) { |
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rnas->Get(i)->mrnas_f[k]->printGff(fout); |
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} |
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for (int k=0;k<rnas->Get(i)->mrnas_r.Count();k++) { |
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rnas->Get(i)->mrnas_r[k]->printGff(fout); |
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} |
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for (int k=0;k<rnas->Get(i)->umrnas.Count();k++) { |
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rnas->Get(i)->umrnas[k]->printGff(fout); |
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} |
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} |
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if (fout!=stdout) fclose(fout); |
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} |
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if (!load_as_ref) delete rnas; |
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} |
