int main(int argc,char ** argv) { Sequence * gen; Genomic * genomic; CodonTable * ct = NULL; GenomeEvidenceSet * ges = NULL; RandomCodonScore * rcs; FILE * ifp = NULL; ComplexSequence * cs = NULL; ComplexSequenceEvalSet * cses = NULL; AlnBlock * alb; PackAln * pal; GenomicRegion * gr; int i; Protein * trans; cDNA * cdna; int kbyte = 10000; int stop_codon_pen = 200; int start_codon_pen = 30; int new_gene = 5000; int switch_cost = 100; int smell = 8; DPRunImpl * dpri = NULL; EstEvidence * est; boolean show_trans = TRUE; boolean show_cdna = FALSE; boolean show_genes = TRUE; boolean show_alb = FALSE; boolean show_pal = FALSE; boolean show_gff = TRUE; boolean show_debug = FALSE; boolean show_geneu = TRUE; char * divide_string = "//"; strip_out_boolean_def_argument(&argc,argv,"geneutr",&show_geneu); strip_out_boolean_def_argument(&argc,argv,"genes",&show_genes); strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans); strip_out_boolean_def_argument(&argc,argv,"gff",&show_gff); strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb); strip_out_boolean_def_argument(&argc,argv,"pal",&show_pal); strip_out_boolean_def_argument(&argc,argv,"debug",&show_debug); strip_out_boolean_def_argument(&argc,argv,"cdna",&show_cdna); strip_out_integer_argument(&argc,argv,"stop",&stop_codon_pen); strip_out_integer_argument(&argc,argv,"start",&start_codon_pen); strip_out_integer_argument(&argc,argv,"gene",&new_gene); strip_out_integer_argument(&argc,argv,"switch",&switch_cost); strip_out_integer_argument(&argc,argv,"smell",&smell); dpri = new_DPRunImpl_from_argv(&argc,argv); if( dpri == NULL ) { fatal("Unable to build DPRun implementation. Bad arguments"); } strip_out_standard_options(&argc,argv,show_help,show_version); if( argc != 3 ) { show_help(stdout); exit(12); } ct = read_CodonTable_file("codon.table"); gen = read_fasta_file_Sequence(argv[1]); ifp = openfile(argv[2],"r"); ges = read_est_evidence(ifp,ct); for(i=0;i<ges->len;i++) { est = (EstEvidence *) ges->geu[i]->data; est->in_smell = smell; } rcs= RandomCodonScore_alloc(); for(i=0;i<125;i++) { if( is_stop_codon(i,ct) ) { rcs->codon[i] = -1000000; } else { rcs->codon[i] = 0; } /* fprintf(stderr,"Got %d for %d\n",rcs->codon[i],i); */ } cses = default_genomic_ComplexSequenceEvalSet(); cs = new_ComplexSequence(gen,cses); pal = PackAln_bestmemory_GenomeWise9(ges,cs,-switch_cost,-new_gene,-start_codon_pen,-stop_codon_pen,rcs,NULL,dpri); alb = convert_PackAln_to_AlnBlock_GenomeWise9(pal); genomic = Genomic_from_Sequence(gen); gr = new_GenomicRegion(genomic); add_Genes_to_GenomicRegion_GeneWise(gr,1,gen->len,alb,gen->name,0,NULL); if( show_genes ) { show_pretty_GenomicRegion(gr,0,stdout); fprintf(stdout,"%s\n",divide_string); } if( show_gff ) { show_GFF_GenomicRegion(gr,gen->name,"genomwise",stdout); fprintf(stdout,"%s\n",divide_string); } if( show_trans ) { for(i=0;i<gr->len;i++) { if( gr->gene[i]->ispseudo == TRUE ) { fprintf(stdout,"#Gene %d is a pseudo gene - no translation possible\n",i); } else { trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct); write_fasta_Sequence(trans->baseseq,stdout); } } fprintf(stdout,"%s\n",divide_string); } if( show_cdna ) { for(i=0;i<gr->len;i++) { cdna = get_cDNA_from_Transcript(gr->gene[i]->transcript[0]); write_fasta_Sequence(cdna->baseseq,stdout); } fprintf(stdout,"%s\n",divide_string); } if( show_geneu ) { show_utr_exon_genomewise(alb,stdout); fprintf(stdout,"%s\n",divide_string); } if( show_alb ) { mapped_ascii_AlnBlock(alb,id,1,stdout); fprintf(stdout,"%s\n",divide_string); } if( show_debug ) { debug_genomewise(alb,ges,ct,gen,stdout); fprintf(stdout,"%s\n",divide_string); } if( show_pal ) { show_simple_PackAln(pal,stdout); fprintf(stdout,"%s\n",divide_string); } return 0; }
boolean show_output(void) { int i; cDNA * cdna; Protein * trans; GenomicOverlapResults * gor; AlnColumn * alt; if( show_pretty == TRUE ) { show_pretty_aln(); } if( show_match_sum == TRUE ) { show_MatchSummary_genewise_header(ofp); show_MatchSummarySet_genewise(mss,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_pretty_gene == TRUE ) { show_pretty_GenomicRegion(gr,0,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_supp_gene == TRUE ) { show_pretty_GenomicRegion(gr,1,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_embl == TRUE ) { write_Embl_FT_GenomicRegion(gr,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_diana == TRUE ) { write_Diana_FT_GenomicRegion(gr,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_overlap == TRUE ) { gor = Genomic_overlap(gr,embl); show_GenomicOverlapResults(gor,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_trans == TRUE ) { for(i=0;i<gr->len;i++) { if( gr->gene[i]->ispseudo == TRUE ) { fprintf(ofp,"#Gene %d is a pseudo gene - no translation possible\n",i); } else { trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct); write_fasta_Sequence(trans->baseseq,ofp); } } fprintf(ofp,"%s\n",divide_str); } if( show_pep == TRUE ) { alt = alb->start; for(;alt != NULL;) { trans = Protein_from_GeneWise_AlnColumn(gen->baseseq,alt,1,&alt,ct,is_random_AlnColumn_genewise); if ( trans == NULL ) break; write_fasta_Sequence(trans->baseseq,ofp); free_Protein(trans); } fprintf(ofp,"%s\n",divide_str); } if( show_cdna == TRUE ) { for(i=0;i<gr->len;i++) { cdna = get_cDNA_from_Transcript(gr->gene[i]->transcript[0]); write_fasta_Sequence(cdna->baseseq,ofp); } fprintf(ofp,"%s\n",divide_str); } if( show_ace == TRUE ) { show_ace_GenomicRegion(gr,gen->baseseq->name,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_gff == TRUE ) { show_GFF_GenomicRegion(gr,gen->baseseq->name,"GeneWise",ofp); fprintf(ofp,"%s\n",divide_str); } if( show_gene_plain == TRUE ) { show_GenomicRegion(gr,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_AlnBlock == TRUE ) { mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_cumlative_PackAln == TRUE ) { show_bits_and_cumlative_PackAln(pal,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_PackAln == TRUE ) { show_simple_PackAln(pal,ofp); fprintf(ofp,"%s\n",divide_str); } return TRUE; }
int main(int argc,char ** argv) { Sequence * cdna; Sequence * gen; Sequence * active_gen; Sequence * active_cdna; int i; int dstart = -1; int dend = -1; int cstart = -1; int cend = -1; CodonTable * ct = NULL; CodonMatrixScore * cm = NULL; RandomCodon * rndcodon = NULL; RandomCodonScore * rndcodonscore = NULL; DnaMatrix * dm = NULL; DPRunImpl * dpri = NULL; GeneModel * gm; GeneModelParam * gmp; GeneStats * gs; GeneParser21 * gp21; GeneParser21Score * gp21s; GeneParser4Score * gp; ComplexSequenceEvalSet * cdna_cses; ComplexSequenceEvalSet * gen_cses; ComplexSequence * cs_cdna; ComplexSequence * cs_gen; Genomic * gent; GenomicRegion * gr; CompMat * cmat; CompProb * cprob; char * matfile = "blosum62.bla"; Protein * trans; PackAln * pal; AlnBlock * alb; FILE * ofp = stdout; dpri = new_DPRunImpl_from_argv(&argc,argv); gmp = new_GeneModelParam_from_argv(&argc,argv); strip_out_integer_argument(&argc,argv,"u",&dstart); strip_out_integer_argument(&argc,argv,"v",&dend); strip_out_integer_argument(&argc,argv,"s",&cstart); strip_out_integer_argument(&argc,argv,"t",&cend); strip_out_standard_options(&argc,argv,show_help,show_version); ct = read_CodonTable_file(codon_file); cmat = read_Blast_file_CompMat(matfile); cprob = CompProb_from_halfbit(cmat); cm = naive_CodonMatrixScore_from_prob(ct,cprob); gm = GeneModel_from_GeneModelParam(gmp); cdna = read_fasta_file_Sequence(argv[1]); gen = read_fasta_file_Sequence(argv[2]); if( dstart != -1 || dend != -1 ) { if( dstart == -1 ) { dstart = 1; } if( dend == -1 ) { dend = gen->len; } active_gen = magic_trunc_Sequence(gen,dstart,dend); } else { active_gen = hard_link_Sequence(gen); } if( cstart != -1 || cend != -1 ) { if( cstart == -1 ) { cstart = 1; } if( cend == -1 ) { cend = gen->len; } active_cdna = magic_trunc_Sequence(gen,cstart,cend); } else { active_cdna = hard_link_Sequence(gen); } rndcodon = RandomCodon_from_raw_CodonFrequency(gm->codon,ct); fold_in_RandomModelDNA_into_RandomCodon(rndcodon,gm->rnd); rndcodonscore = RandomCodonScore_from_RandomCodon(rndcodon); assert(active_cdna); assert(active_gen); cdna_cses = default_cDNA_ComplexSequenceEvalSet(); gen_cses = new_ComplexSequenceEvalSet_from_GeneModel(gm); cs_cdna = new_ComplexSequence(active_cdna,cdna_cses); cs_gen = new_ComplexSequence(active_gen,gen_cses); gp21 = std_GeneParser21(); GeneParser21_fold_in_RandomModelDNA(gp21,gm->rnd); gp21s = GeneParser21Score_from_GeneParser21(gp21); gp = GeneParser4Score_from_GeneParser21Score(gp21s); dm = identity_DnaMatrix(Probability2Score(halfbit2Probability(1)),Probability2Score(halfbit2Probability(-1))); assert(cs_cdna); assert(cs_gen); assert(gp); assert(rndcodonscore); assert(dm); assert(dpri); /* show_CodonMatrixScore(cm,ct,ofp);*/ pal = PackAln_bestmemory_CdnaWise10(cs_cdna,cs_gen,gp,cm,rndcodonscore,dm, Probability2Score(halfbit2Probability(-12)), Probability2Score(halfbit2Probability(-2)), Probability2Score(halfbit2Probability(-5)), Probability2Score(halfbit2Probability(0)), NULL, dpri); alb = convert_PackAln_to_AlnBlock_CdnaWise10(pal); gent = Genomic_from_Sequence(gen); assert(gent); gr = new_GenomicRegion(gent); assert(gr); add_Genes_to_GenomicRegion_GeneWise(gr,active_gen->offset,active_gen->end,alb,cdna->name,0,NULL); mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp); show_pretty_GenomicRegion(gr,0,ofp); for(i=0;i<gr->len;i++) { if( gr->gene[i]->ispseudo == TRUE ) { fprintf(ofp,"#Gene %d is a pseudo gene - no translation possible\n",i); } else { trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct); write_fasta_Sequence(trans->baseseq,ofp); } } }