int main(int argc,char ** argv) { GenoVarSet * s; PackAln * pal; AlnBlock * alb; DPRunImpl * dpri; SnpMatch * snpm; int i; GenomePara * p; MouseSNPMatch * forward; MouseSNPMatch * backward; FILE * ifp; dpri = new_DPRunImpl_from_argv(&argc,argv); strip_out_standard_options(&argc,argv,show_help,show_version); ifp = openfile(argv[1],"r"); assert(ifp != NULL); s = read_sanger_genotype_file(ifp); p = new_GenomePara(0.95,0.01); fprintf(stdout,"Score for match %d, score for mismatch %d\n",p->match,p->mismatch); for(i=0;i < s->len ;i++) { snpm = new_SnpMatch(s->chr[i],s,"DBA","PWK","CAST","WSB"); /* show_SnpMatchStats(snpm,stdout); */ backward = backward_logsum_MouseSNPMatch(p,snpm,dpri); forward = forward_logsum_MouseSNPMatch(p,snpm,dpri); fprintf(stdout,"Backward score is %d\n", MouseSNPMatch_EXPL_SPECIAL(backward,0,-1,0)); fprintf(stdout,"Forward score is %d Backward score is %d\n",MouseSNPMatch_EXPL_SPECIAL(forward,0,forward->lenj-1,1), MouseSNPMatch_EXPL_SPECIAL(backward,0,-1,0)); } }
int main (int argc,char ** argv) { EditString * q; EditString * t; PackAln * pal; AlnBlock * alb; int match = 1; int mismatch = -1; int gap = -1; boolean show_pretty = FALSE; DPRunImpl * dpri = NULL; StandardOutputOptions * std_opt = NULL; strip_out_boolean_def_argument(&argc,argv,"pretty",&show_pretty); dpri = new_DPRunImpl_from_argv(&argc,argv); std_opt = new_StandardOutputOptions_from_argv(&argc,argv); if( dpri == NULL ) { fatal("Unable to build DPRun implementation. Bad arguments"); } if( argc != 3 ) { show_help(stdout); exit(12); } q = new_EditString(argv[1]); t = new_EditString(argv[2]); pal = PackAln_bestmemory_EditDistance(q,t,match,mismatch,gap,NULL,dpri); alb = convert_PackAln_to_AlnBlock_EditDistance(pal); fprintf(stdout,"Score %d\n",pal->score); if( show_pretty == TRUE ) { write_pretty_str_align(alb,"string1",q->string,"string2",t->string,12,60,stdout); } show_StandardOutputOptions(std_opt,alb,pal,"//",stdout); return 0; }
int main(int argc,char ** argv) { SignalMap * map; int i; FILE * sm; Sequence * seq; SignalSeq * ss; FILE * sseqf; PackAln * pal; AlnBlock * alb; DPRunImpl * dpri; srandomdev(); sm = openfile(argv[1],"r"); dpri = new_DPRunImpl_from_argv(&argc,argv); map = read_SignalMap(sm); seq = read_fasta_file_Sequence(argv[2]); sseqf = openfile(argv[3],"r"); ss = read_SignalSeq(sseqf); assert(map != NULL); assert(seq != NULL); assert(ss != NULL); pal = PackAln_bestmemory_SimpleSignalMat(ss,seq,map,-10,-2,NULL,dpri); alb = convert_PackAln_to_AlnBlock_SimpleSignalMat(pal); show_alignment_with_fit_SimpleSignalMat(alb,ss,seq,map,stdout); }
DnaProfileEnginePara * new_DnaProfileEnginePara_from_argv(int * argc,char ** argv) { DnaProfileEnginePara * out; out = DnaProfileEnginePara_alloc(); out->dpri = new_DPRunImpl_from_argv(argc,argv); out->setpara = new_LocalCisHitSetPara_from_argv(argc,argv); out->lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); out->rm = RandomModelDNA_std(); out->pseudo = 0.5; out->open_unmatched = 0.001; out->ext_unmatched = 0.8; out->gap_unmatched = 0.5; out->seq_id = 0.8; out->m2i = 0.1; out->m2d = 0.1; out->i2i = 0.8; out->d2d = 0.8; out->min_seq_prof = 400; strip_out_float_argument(argc,argv,"dnap_pseudo",&out->pseudo); strip_out_float_argument(argc,argv,"dnap_open_un",&out->open_unmatched); strip_out_float_argument(argc,argv,"dnap_ext_un",&out->ext_unmatched); strip_out_float_argument(argc,argv,"dnap_gap_un",&out->ext_unmatched); strip_out_float_argument(argc,argv,"dnap_seq_self",&out->seq_id); strip_out_float_argument(argc,argv,"dnap_m2i",&out->m2i); strip_out_float_argument(argc,argv,"dnap_m2d",&out->m2d); strip_out_float_argument(argc,argv,"dnap_i2i",&out->i2i); strip_out_float_argument(argc,argv,"dnap_d2d",&out->d2d); strip_out_integer_argument(argc,argv,"dnap_min_seq_prof",&out->min_seq_prof); return out; }
int main(int argc,char ** argv) { int i; char * temp; build_defaults(); strip_out_standard_options(&argc,argv,show_help,show_version); potential_file = strip_out_assigned_argument(&argc,argv,"pg"); pal_file = strip_out_assigned_argument(&argc,argv,"pal_file"); if( (temp = strip_out_assigned_argument(&argc,argv,"gap")) != NULL ) gap_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"g")) != NULL ) gap_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"ext")) != NULL ) ext_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"e")) != NULL ) ext_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"matrix")) != NULL ) matrix_file = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"m")) != NULL ) matrix_file = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"s")) != NULL ) qstart_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"t")) != NULL ) qend_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"u")) != NULL ) tstart_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"v")) != NULL ) tend_str = temp; if( (strip_out_boolean_argument(&argc,argv,"trev")) == TRUE ) reverse = TRUE; if( (strip_out_boolean_argument(&argc,argv,"[no]newgene")) == TRUE ) use_new_stats = TRUE; if( (strip_out_boolean_argument(&argc,argv,"tfor")) == TRUE ){ if( reverse == TRUE ) { warn("You have specified both trev and tfor. Treating as both"); do_both = TRUE; reverse = FALSE; } else { reverse = FALSE; } } if( (temp = strip_out_assigned_argument(&argc,argv,"insert")) != NULL ) { if( strcmp(temp,"flat") == 0 ) { flat_insert = TRUE; } else { flat_insert = FALSE; } } if( (strip_out_boolean_argument(&argc,argv,"both")) == TRUE ) do_both = TRUE; if( (strip_out_boolean_argument(&argc,argv,"fembl")) == TRUE ) is_embl = TRUE; if( (strip_out_boolean_argument(&argc,argv,"tabs")) == TRUE ) target_abs = TRUE; pseudo = strip_out_boolean_argument(&argc,argv,"pseudo"); if( (temp = strip_out_assigned_argument(&argc,argv,"codon")) != NULL ) codon_file = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"gene")) != NULL ) gene_file = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"alg")) != NULL ) alg_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"kbyte")) != NULL ) kbyte_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"subs")) != NULL ) subs_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"indel")) != NULL ) indel_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"cfreq")) != NULL ) cfreq_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"splice")) != NULL ) { warn("deprecated command line option -splice. use -splice_gtag now"); splice_string = temp; } if( (temp = strip_out_assigned_argument(&argc,argv,"init")) != NULL ) startend_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"null")) != NULL ) null_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"intron")) != NULL ) intron_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"alln")) != NULL ) allN_string = temp; if( (strip_out_boolean_argument(&argc,argv,"hmmer")) == TRUE ) use_tsm = TRUE; if( (strip_out_boolean_argument(&argc,argv,"intie")) == TRUE ) use_tied_model = TRUE; if( (temp = strip_out_assigned_argument(&argc,argv,"hname")) != NULL ) hmm_name = temp; if( (strip_out_boolean_argument(&argc,argv,"pretty")) != FALSE ) show_pretty = TRUE; if( (strip_out_boolean_argument(&argc,argv,"gff")) != FALSE ) show_gff = TRUE; if( (strip_out_boolean_argument(&argc,argv,"diana")) != FALSE ) show_diana = TRUE; if( (strip_out_boolean_argument(&argc,argv,"embl")) != FALSE ) show_embl = TRUE; if( (strip_out_boolean_argument(&argc,argv,"genes")) != FALSE ) show_pretty_gene = TRUE; if( (strip_out_boolean_argument(&argc,argv,"genesf")) != FALSE ) show_supp_gene = TRUE; if( (strip_out_boolean_argument(&argc,argv,"para")) != FALSE ) show_para = TRUE; if( (strip_out_boolean_argument(&argc,argv,"trans")) != FALSE ) show_trans = TRUE; if( (strip_out_boolean_argument(&argc,argv,"pep")) != FALSE ) show_pep = TRUE; if( (strip_out_boolean_argument(&argc,argv,"cdna")) != FALSE ) show_cdna = TRUE; if( (strip_out_boolean_argument(&argc,argv,"sum")) != FALSE ) show_match_sum = TRUE; if( (strip_out_boolean_argument(&argc,argv,"alb")) != FALSE ) show_AlnBlock = TRUE; if( (strip_out_boolean_argument(&argc,argv,"ace")) != FALSE ) show_ace = TRUE; if( (strip_out_boolean_argument(&argc,argv,"pal")) != FALSE ) show_PackAln = TRUE; if( (strip_out_boolean_argument(&argc,argv,"gener")) != FALSE ) show_gene_plain = TRUE; if( (strip_out_boolean_argument(&argc,argv,"over")) != FALSE ) show_overlap = TRUE; if( (temp = strip_out_assigned_argument(&argc,argv,"divide")) != NULL ) divide_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"block")) != NULL ) main_block_str = temp; dpri = new_DPRunImpl_from_argv(&argc,argv); gmp = new_GeneModelParam_from_argv(&argc,argv); ppp = new_PhasedProteinPara_from_argv(&argc,argv); gwrp = new_GeneWiseRunPara_from_argv(&argc,argv); strip_out_remaining_options_with_warning(&argc,argv); if( argc != 3 ) { warn("Wrong number of arguments (expect 2)!\n"); if( argc > 1 ){ warn("Arg line looked like (after option processing)"); for(i=1;i<argc;i++) { fprintf(stderr," %s\n",argv[i]); } } show_short_help(); } if( show_embl == FALSE && show_diana == FALSE && show_gff == FALSE && show_overlap == FALSE && show_pretty_gene == FALSE && show_match_sum == FALSE && show_ace == FALSE && show_gene_plain == FALSE && show_pretty == FALSE && show_AlnBlock == FALSE && show_PackAln == FALSE && show_pep == FALSE ) { show_pretty = TRUE; show_para = TRUE; } dna_seq_file = argv[2]; if( use_tsm == FALSE) protein_file = argv[1]; else hmm_file = argv[1]; if( build_objects() == FALSE) fatal("Could not build objects!"); if( show_para == TRUE) { show_parameters(); } if( build_alignment() == FALSE) fatal("Could not build alignment!"); if( show_output() == FALSE) fatal("Could not show alignment. Sorry!"); if( do_both == TRUE) { reverse_target(); if( build_alignment() == FALSE) fatal("Could not build alignment!"); if( show_output() == FALSE) fatal("Could not show alignment. Sorry!"); } free_temporary_objects(); free_io_objects(); return 0; }
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; }
int main(int argc,char ** argv) { int i; char * temp; build_defaults(); bootstrap_HMMer2(); strip_out_standard_options(&argc,argv,show_help,show_version); if( (temp = strip_out_assigned_argument(&argc,argv,"gap")) != NULL ) gap_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"g")) != NULL ) gap_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"ext")) != NULL ) ext_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"e")) != NULL ) ext_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"matrix")) != NULL ) matrix_file = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"m")) != NULL ) matrix_file = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"s")) != NULL ) qstart_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"t")) != NULL ) qend_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"aln")) != NULL ) aln_number_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"codon")) != NULL ) codon_file = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"alg")) != NULL ) alg_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"aalg")) != NULL ) aln_alg_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"cut")) != NULL ) search_cutoff_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"ecut")) != NULL ) evalue_search_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"subs")) != NULL ) subs_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"indel")) != NULL ) indel_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"init")) != NULL ) startend_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"alln")) != NULL ) allN_string = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"null")) != NULL ) null_string = temp; if( (strip_out_boolean_argument(&argc,argv,"dnas")) == TRUE ) use_single_dna = TRUE; if( (strip_out_boolean_argument(&argc,argv,"dnadb")) == TRUE ) use_single_dna = FALSE; if( (strip_out_boolean_argument(&argc,argv,"tfor")) == TRUE ) do_forward_only = TRUE; if( (strip_out_boolean_argument(&argc,argv,"flati")) == TRUE ) flat_insert = TRUE; if( (strip_out_boolean_argument(&argc,argv,"hmmer")) == TRUE ) use_tsm = TRUE; if( (strip_out_boolean_argument(&argc,argv,"pfam2")) == TRUE ) use_pfam1 = TRUE; if( (strip_out_boolean_argument(&argc,argv,"pfam")) == TRUE ) use_pfam2 = TRUE; if( (strip_out_boolean_argument(&argc,argv,"protein")) == TRUE ) use_single_pro = TRUE; if( (strip_out_boolean_argument(&argc,argv,"prodb")) == TRUE ) use_db_pro = TRUE; if( (temp = strip_out_assigned_argument(&argc,argv,"hname")) != NULL ) hmm_name = temp; if( (strip_out_boolean_argument(&argc,argv,"nohis")) != FALSE ) show_histogram = FALSE; if( (strip_out_boolean_argument(&argc,argv,"pretty")) != FALSE ) show_pretty = TRUE; if( (strip_out_boolean_argument(&argc,argv,"pep")) != FALSE ) show_pep = TRUE; if( (strip_out_boolean_argument(&argc,argv,"mul")) != FALSE ) make_anchored_aln = TRUE; if( (strip_out_boolean_argument(&argc,argv,"para")) != FALSE ) show_para = TRUE; if( (strip_out_boolean_argument(&argc,argv,"sum")) != FALSE ) show_match_sum = TRUE; if( (strip_out_boolean_argument(&argc,argv,"alb")) != FALSE ) show_AlnBlock = TRUE; if( (strip_out_boolean_argument(&argc,argv,"pal")) != FALSE ) show_PackAln = TRUE; if( (temp = strip_out_assigned_argument(&argc,argv,"divide")) != NULL ) divide_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"block")) != NULL ) main_block_str = temp; if( (temp = strip_out_assigned_argument(&argc,argv,"report")) != NULL ) report_str = temp; dbsi = new_DBSearchImpl_from_argv(&argc,argv); dpri = new_DPRunImpl_from_argv(&argc,argv); strip_out_remaining_options_with_warning(&argc,argv); if( argc != 3 ) { warn("Wrong number of arguments (expect 2)!\n"); if( argc > 1 ){ warn("Arg line looked like (after option processing)"); for(i=1;i<argc;i++) { fprintf(stderr," %s\n",argv[i]); } } show_short_help(); } if( show_pretty == FALSE && show_AlnBlock == FALSE && show_PackAln == FALSE && show_pep == FALSE ) { show_pretty = TRUE; show_para = TRUE; } if( use_db_pro == FALSE && use_single_pro == FALSE && use_tsm == FALSE && use_pfam1 == FALSE && use_pfam2 == FALSE ) { use_single_pro = TRUE; } if( use_single_pro == TRUE || use_tsm == TRUE ) { if( use_single_dna == TRUE ) fatal("one on one search. Shouldn't you use pcwise?"); search_mode = PC_SEARCH_S2DB; } else { if( use_single_dna == TRUE ) search_mode = PC_SEARCH_DB2S; else search_mode = PC_SEARCH_DB2DB; } if( evalue_search_str != NULL && search_mode != PC_SEARCH_S2DB ) { fatal("Trying to set a evalue cutoff on a non evalue based search. you can only use evalues in a protein HMM vs DNA database search (sorry!)"); } if( make_anchored_aln == TRUE && search_mode != PC_SEARCH_S2DB ) { fatal("Trying to make an anchored alignment and not in single search mode"); } if( make_anchored_aln == TRUE) { do_complete_analysis = TRUE; } /* pick up remaining args and do it */ dna_seq_file = argv[2]; protein_file = argv[1]; if( build_objects() == FALSE) fatal("Could not build objects!"); if( build_db_objects() == FALSE) fatal("Could not build database-ready objects!"); show_header(stdout); if( search_db() == FALSE) warn("Could not search database"); show_output(); free_objects(); return 0; }
int main(int argc,char ** argv) { int type = ALIGN_NORMAL; DPRunImpl * dpri = NULL; HitList * hl; HitListOutputImpl * hloi; Sequence * query; Sequence * target; Sequence * target_rev; PairwiseShortDna * two; LocalCisHitSet * set; LocalCisHitSet * greedy_set; LocalCisHitScore * lchs; LocalCisHitSetPara * setpara; MotifMatrixPara * mmp; MotifMatrixScore * mms; TransFactorMatchSet * tfms_query = NULL; TransFactorMatchSet * tfms_target = NULL; TransFactorMatchSet * tfms_target_rev = NULL; int qstart = -1; int qend = -1; int tstart = -1; int tend = -1; int i; char * temp; DnaMatrix * dm; DnaProbMatrix * dmp; TransFactorBuildPara * tfbp; TransFactorMatchPara * tfmp; TransFactorSet * tfs; char * motif_library = NULL; int use_laurence = FALSE; int use_ben = FALSE; dmp = DnaProbMatrix_from_match(0.75,NMaskType_BANNED); assert(dmp); flat_null_DnaProbMatrix(dmp); dm = DnaMatrix_from_DnaProbMatrix(dmp); dpri = new_DPRunImpl_from_argv(&argc,argv); hloi = new_HitListOutputImpl_from_argv(&argc,argv); setpara = new_LocalCisHitSetPara_from_argv(&argc,argv); mmp = new_MotifMatrixPara_from_argv(&argc,argv); tfbp = new_TransFactorBuildPara_from_argv(&argc,argv); tfmp = new_TransFactorMatchPara_from_argv(&argc,argv); strip_out_integer_argument(&argc,argv,"s",&qstart); strip_out_integer_argument(&argc,argv,"t",&qend); strip_out_integer_argument(&argc,argv,"u",&tstart); strip_out_integer_argument(&argc,argv,"v",&tend); temp = strip_out_assigned_argument(&argc,argv,"motiflib"); if( temp != NULL ) { motif_library = stringalloc(temp); } use_laurence = strip_out_boolean_argument(&argc,argv,"lr"); use_ben = strip_out_boolean_argument(&argc,argv,"ben"); temp = strip_out_assigned_argument(&argc,argv,"align"); if( temp != NULL ) { if( strcmp(temp,"motif") == 0 ) { type = ALIGN_MOTIF; } else if ( strcmp(temp,"normal") == 0 ) { type = ALIGN_NORMAL; } else { fatal("cannot recognise string %s as align type",temp); } } strip_out_standard_options(&argc,argv,show_help,show_version); if( argc != 3 ) { show_help(stdout); exit(12); } lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); query = read_fasta_file_Sequence(argv[1]); target = read_fasta_file_Sequence(argv[2]); for(i=0;i<query->len;i++) { query->seq[i] = toupper(query->seq[i]); } assert(query != NULL); assert(target != NULL); target_rev = reverse_complement_Sequence(target); mms = MotifMatrixScore_from_MotifMatrixPara(mmp); if( type == ALIGN_MOTIF ) { if( motif_library == NULL ) { fatal("Wanted to align with motif but not motif library. Must use -motiflib"); } if( use_laurence == TRUE ) { tfs = read_laurence_TransFactorSet_file(motif_library); } else if( use_ben == TRUE ) { tfs = read_ben_IUPAC_TransFactorSet_file(motif_library); } else { tfs = read_TransFactorSet_file(motif_library); } build_TransFactorSet(tfs,tfbp); tfms_query = calculate_TransFactorMatchSet(query,tfs,tfmp); sort_by_start_TransFactorMatchSet(tfms_query); tfms_target = calculate_TransFactorMatchSet(target,tfs,tfmp); sort_by_start_TransFactorMatchSet(tfms_target); tfms_target_rev = calculate_TransFactorMatchSet(target_rev,tfs,tfmp); sort_by_start_TransFactorMatchSet(tfms_target); fprintf(stdout,"Motif Set: %d in query and %d in target\n",tfms_query->len,tfms_target->len); } if( qstart == -1 ) { qstart = 0; } if( qend == -1 ) { qend = query->len; } if( tstart == -1 ) { tstart = 0; } if( tend == -1 ) { tend = target->len; } two = query_to_reverse_target(query,target,dm,qstart,qend,tstart,tend); set = make_LocalCisHitSet(query,target,target_rev,two->forward,two->reverse,setpara,lchs,tfms_query,tfms_target,tfms_target_rev,mms,type == ALIGN_MOTIF ? 1 : 0,dpri); greedy_set = greedy_weed_LocalCisHitSet(set,setpara); hl = HitList_from_LocalCisHitSet(greedy_set); show_HitList_HitListOutputImpl(hloi,hl,stdout); return 0; }
int main(int argc,char ** argv) { DPRunImpl * dpri = NULL; ScanWiseHSPImpl * scani = NULL; HSP2HitListImpl * hsp2hiti = NULL; HitListOutputImpl * hloi = NULL; ProteinIndexConstructor * pic = NULL; HSPScanInterface * hsi; HSPScanInterfacePara * para; SearchStatInterface * ssi; SearchStatInterface * ssl; SeqLookupLoadPara * slp; HSPset2HitPairPara * hsp2hit; CompMat * mat; SequenceDB * db; Sequence * seq; int ret; int i; int effective_db_size = 300000; int kk; int count = 0; LinearHSPmanager * lm; HitList * hl; boolean use_mott = 1; boolean trunc_best_hsp = 0; boolean verbose = 0; static struct rusage use; struct timeval t0, t1; gettimeofday(&t0, NULL); dpri = new_DPRunImpl_from_argv(&argc,argv); dpri->memory = DPIM_Explicit; scani = new_ScanWiseHSPImpl_from_argv(&argc,argv); hsp2hiti = new_HSP2HitListImpl_from_argv(&argc,argv); hloi = new_HitListOutputImpl_from_argv(&argc,argv); slp = new_SeqLookupLoadPara_from_argv(&argc,argv); pic = new_ProteinIndexConstructor_from_argv(&argc,argv); hsp2hit = new_HSPset2HitPairPara_from_argv(&argc,argv); para = new_HSPScanInterfacePara_from_argv(&argc,argv); verbose = strip_out_boolean_argument(&argc,argv,"verbose") ; strip_out_boolean_def_argument(&argc,argv,"mott",&use_mott); strip_out_boolean_def_argument(&argc,argv,"besthsp",&trunc_best_hsp); strip_out_integer_argument(&argc,argv,"dbsize",&effective_db_size); #ifdef SCAN_CORBA sorb = get_Wise2Corba_Singleton(&argc,argv,"orbit-local-orb"); #endif if( dpri == NULL ) { fatal("Unable to build DPRun implementation. Bad arguments"); } strip_out_standard_options(&argc,argv,show_help,show_version); if( argc != 2 ) { show_help(stdout); exit(12); } /* ugly, but we don't want to bounce matrices around the network... */ mat = read_Blast_file_CompMat("BLOSUM62.bla"); erroroff(REPORT); hsi = new_HSPScanInterface_from_ScanWiseHSPImpl(scani,pic,slp); ssi = new_Mott_SearchStatInterface(); ssl = new_lookup_SearchStatInterface(40,2.3); if( verbose ) { info("contacted database"); } db = single_fasta_SequenceDB(argv[1]); if( db == NULL ) { fatal("Could not open sequence db...\n"); } for(seq = init_SequenceDB(db,&ret); seq != NULL;seq = get_next_SequenceDB(db) ) { count++; for(i=0;i<seq->len;i++) { if( !isalpha(seq->seq[i]) ) { fatal("Sequence position %d [%c] is not valid",i,seq->seq[i]); } seq->seq[i] = toupper(seq->seq[i]); } info("Processing %s",seq->name); getrusage(RUSAGE_SELF,&use); /* info("Before query %s %.3fu %.3fs\n", seq->name, use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND, use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND ); */ lm = (*hsi->scan_query)(hsi->data,seq,para); fprintf(stderr,"Got linear manager is %d entries\n",lm->len); if( lm->mat == NULL ) { lm->mat = hard_link_CompMat(mat); } getrusage(RUSAGE_SELF,&use); /* info("After query %s %.3fu %.3fs\n", seq->name, use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND, use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND ); */ sort_LinearHSPmanager(lm,compare_HSPset_score); if( trunc_best_hsp == 1 ) { for(kk=1;kk<lm->len;kk++) { free_HSPset(lm->set[kk]); lm->set[kk] = NULL; } lm->len = 1; } getrusage(RUSAGE_SELF,&use); /* info("After sort %s %.3fu %.3fs\n", seq->name, use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND, use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND ); */ hl = HitList_from_HSP_HSP2HitListImpl(hsp2hiti,lm,dpri,hsp2hit); getrusage(RUSAGE_SELF,&use); /* info("After conversion %s %.3fu %.3fs\n", seq->name, use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND, use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND ); */ free_LinearHSPmanager(lm); if( use_mott == 1 ) { apply_SearchStat_to_HitList(hl,ssi,effective_db_size); } else { for(kk=0;kk<hl->len;kk++) { hl->pair[kk]->bit_score = hl->pair[kk]->raw_score / 2.0; } } sort_HitList_by_score(hl); show_HitList_HitListOutputImpl(hloi,hl,stdout); getrusage(RUSAGE_SELF,&use); /* info("After output %s %.3fu %.3fs\n", seq->name, use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND, use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND ); */ free_HitList(hl); free_Sequence(seq); } free_DPRunImpl(dpri); free_HSPScanInterface(hsi); gettimeofday(&t1, NULL); fprintf(stderr, "[client stats] queries, time (s): %d %f\n", count, (t1.tv_sec - t0.tv_sec) + (t1.tv_usec - t0.tv_usec) * 1e-6); return 0; }
int main(int argc,char ** argv) { Sequence * query; Sequence * target; CompMat * comp; char * comp_file; int gap = (12); int ext = (2); int a = 120; int b = 10; int c = 3; ComplexSequence * query_cs; ComplexSequence * target_cs; ComplexSequenceEvalSet * evalfunc; boolean show_label_output = FALSE; boolean show_fancy_output = FALSE; boolean use_abc = FALSE; PackAln * pal; AlnBlock * alb; DPRunImpl * dpri = NULL; /* * Process command line options * -h or -help gives us help * -g for gap value (an int) - rely on commandline error processing * -e for ext value (an int) - rely on commandline error processing * -m for matrix (a char) * -l - label output * -f - fancy output * * * Use calls to commandline.h functions * */ if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) { show_help(stdout); exit(1); } dpri = new_DPRunImpl_from_argv(&argc,argv); if( dpri == NULL ) { fatal("Unable to build DPRun implementation. Bad arguments"); } show_label_output = strip_out_boolean_argument(&argc,argv,"l"); show_fancy_output = strip_out_boolean_argument(&argc,argv,"f"); /** if all FALSE, set fancy to TRUE **/ if( show_label_output == FALSE ) show_fancy_output = TRUE; (void) strip_out_integer_argument(&argc,argv,"g",&gap); (void) strip_out_integer_argument(&argc,argv,"e",&ext); (void) strip_out_integer_argument(&argc,argv,"a",&a); (void) strip_out_integer_argument(&argc,argv,"b",&b); (void) strip_out_integer_argument(&argc,argv,"c",&c); use_abc = strip_out_boolean_argument(&argc,argv,"abc"); comp_file = strip_out_assigned_argument(&argc,argv,"m"); if( comp_file == NULL) comp_file = "blosum62.bla"; if( argc != 3 ) { warn("Must have two arguments for sequence 1 and sequence 2 %d",argc); show_help(stdout); exit(1); } /* * Read in two sequences */ if( (query=read_fasta_file_Sequence(argv[1])) == NULL ) { fatal("Unable to read the sequence in file %s",argv[1]); } if( (target=read_fasta_file_Sequence(argv[2])) == NULL ) { fatal("Unable to read the sequence in file %s",argv[2]); } /* * Open a blosum matrix. This will be opened from WISECONFIGDIR * or WISEPERSONALDIR if it is not present in the current directory. */ comp = read_Blast_file_CompMat(comp_file); if( comp == NULL ) { fatal("unable to read file %s",comp_file); } /* if abc - factor up matrix! */ if( use_abc == TRUE ) { factor_CompMat(comp,10); } /* * Make an alignment. I don't care about the implementation: * hand it over to sw_wrap function to do it * */ if( use_abc ) { evalfunc = default_aminoacid_ComplexSequenceEvalSet(); query_cs = new_ComplexSequence(query,evalfunc); if( query_cs == NULL ) fatal("Cannot build cs objects!"); target_cs = new_ComplexSequence(target,evalfunc); if( target_cs == NULL ) fatal("Cannot build cs objects!"); pal = PackAln_bestmemory_abc(query_cs,target_cs,comp,-a,-b,-c,NULL,dpri); alb = convert_PackAln_to_AlnBlock_abc(pal); free_ComplexSequence(query_cs); free_ComplexSequence(target_cs); } else { alb = Align_Sequences_ProteinSmithWaterman(query,target,comp,-gap,-ext,dpri); } /* * show output. If multiple outputs, divide using // */ if( show_label_output == TRUE ) { show_flat_AlnBlock(alb,stdout); puts("//\n"); } if( show_fancy_output == TRUE ) { write_pretty_seq_align(alb,query,target,15,50,stdout); puts("//\n"); } /* * Destroy the memory. */ free_Sequence(query); free_Sequence(target); free_CompMat(comp); free_AlnBlock(alb); return 0; }
int main(int argc,char ** argv) { int i; DPRunImpl * dpri = NULL; GeneModelParam * gmp = NULL; GeneModel * gm = NULL; Sequence * seq; RandomCodon * rc; RandomModelDNA * rmd; RandomCodonScore * rcs; ComplexSequenceEval * splice5; ComplexSequenceEval * splice3; ComplexSequenceEvalSet * cses; ComplexSequence * cseq; SyExonScore * exonscore; PackAln * pal; AlnBlock * alb; Genomic * genomic; GenomicRegion * gr; Protein * trans; dpri = new_DPRunImpl_from_argv(&argc,argv); if( dpri == NULL ) { fatal("Unable to build DPRun implementation. Bad arguments"); } gmp = new_GeneModelParam_from_argv(&argc,argv); ct= read_CodonTable_file("codon.table"); strip_out_standard_options(&argc,argv,show_help,show_version); if( argc != 2 ) { show_help(stdout); exit(12); } if((gm=GeneModel_from_GeneModelParam(gmp)) == NULL ) { fatal("Could not build gene model"); } seq = read_fasta_file_Sequence(argv[1]); assert(seq); cses = new_ComplexSequenceEvalSet_from_GeneModel(gm); cseq = new_ComplexSequence(seq,cses); rc = flat_RandomCodon(ct); rmd = RandomModelDNA_std(); fold_in_RandomModelDNA_into_RandomCodon(rc,rmd); rcs = RandomCodonScore_from_RandomCodon(rc); exonscore = SyExonScore_flat_model(200,250,0.1,0.1); /* for(i=0;i<cseq->length;i++) { fprintf(stdout,"%d PairSeq is %d score %d\n",i,CSEQ_PAIR_PAIRBASE(cseq,i),nonc_score->base[CSEQ_PAIR_PAIRBASE(cseq,i)]); } exit(0); */ /* show_RandomCodonScore(rcs,stdout); for(i=3;i<seq->len;i++) { fprintf(stdout,"seq %d is %c with score %d\n",i,aminoacid_from_seq(ct,seq->seq+i-2),rcs->codon[CSEQ_GENOMIC_CODON(cseq,i)]); } exit(0); */ pal = PackAln_bestmemory_StatWise10(exonscore,cseq,rcs,Probability2Score(1.0/10.0),Probability2Score(1.0/10.0),NULL,dpri); alb = convert_PackAln_to_AlnBlock_StatWise10(pal); mapped_ascii_AlnBlock(alb,id,1,stdout); genomic = Genomic_from_Sequence(seq); gr = new_GenomicRegion(genomic); add_Genes_to_GenomicRegion_GeneWise(gr,1,seq->len,alb,"bollocks",0,NULL); 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); } } return 0; }
int main(int argc,char ** argv) { int i; SequenceSet * in; Sequence * trans; ThreeStateDB * tsd; DPRunImpl * dpri; CodonTable * ct; int return_status; ThreeStateModel * tsm; ThreeStateScore * tss; Protein * hmmp; ComplexSequence * cs; ComplexSequenceEvalSet * cses; PackAln * pal; AlnBlock * alb; int show_align = 0; int show_alb = 0; int show_verbose = 1; int show_trans = 0; ct = read_CodonTable_file("codon.table"); cses = default_aminoacid_ComplexSequenceEvalSet(); dpri = new_DPRunImpl_from_argv(&argc,argv); strip_out_boolean_def_argument(&argc,argv,"pretty",&show_align); strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb); strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans); if( argc != 3 ) { show_help(stdout); exit(63); } in = read_fasta_SequenceSet_file(argv[1]); tsd = HMMer2_ThreeStateDB(argv[2]); assert(in); assert(tsd); assert(in->len == 2); trans = translate_Sequence(in->set[0],ct); if( show_trans ) { write_fasta_Sequence(trans,stdout); } cs = new_ComplexSequence(trans,cses); open_ThreeStateDB(tsd); while( (tsm = read_TSM_ThreeStateDB(tsd,&return_status)) != NULL ) { fold_RandomModel_into_ThreeStateModel(tsm,tsm->rm); set_startend_policy_ThreeStateModel(tsm,TSM_local,10,1.0); tss = ThreeStateScore_from_ThreeStateModel(tsm); hmmp = pseudo_Protein_from_ThreeStateModel(tsm); pal = PackAln_bestmemory_ThreeStateLoop(tss,cs,NULL,dpri); alb = convert_PackAln_to_AlnBlock_ThreeStateLoop(pal); if( show_alb ) { show_flat_AlnBlock(alb,stdout); } if( show_align ) { write_pretty_seq_align(alb,hmmp->baseseq,trans,15,50,stdout); } if( show_verbose ) { show_verbose_evo(alb,tsm,in->set[0],in->set[1],ct,stdout); } } }
int main(int argc,char ** argv) { int i; DPRunImpl * dpri = NULL; GeneModelParam * gmp = NULL; GeneModel * gm = NULL; FILE * ifp; SeqAlign * al; PairBaseSeq * pbs; ComplexSequenceEval * splice5; ComplexSequenceEval * splice3; ComplexSequence * cseq; CompMat * score_mat; CompProb * comp_prob; RandomModel * rm; PairBaseCodonModelScore * codon_score; PairBaseModelScore* nonc_score; PairBaseCodonModelScore * start; PairBaseCodonModelScore * stop; SyExonScore * exonscore; PackAln * pal; AlnBlock * alb; Genomic * genomic; GenomicRegion * gr; GenomicRegion * gr2; Protein * trans; StandardOutputOptions * std_opt; ShowGenomicRegionOptions * sgro; char * dump_packaln = NULL; char * read_packaln = NULL; FILE * packifp = NULL; boolean show_trans = 1; boolean show_gene_raw = 0; ct = read_CodonTable_file(codon_table); /* score_mat = read_Blast_file_CompMat("blosum62.bla"); comp_prob = CompProb_from_halfbit(score_mat); */ rm = default_RandomModel(); comp_prob = read_Blast_file_CompProb("wag85"); fold_column_RandomModel_CompProb(comp_prob,rm); dpri = new_DPRunImpl_from_argv(&argc,argv); if( dpri == NULL ) { fatal("Unable to build DPRun implementation. Bad arguments"); } gmp = new_GeneModelParam_from_argv(&argc,argv); std_opt = new_StandardOutputOptions_from_argv(&argc,argv); sgro = new_ShowGenomicRegionOptions_from_argv(&argc,argv); dump_packaln = strip_out_assigned_argument(&argc,argv,"dump"); read_packaln = strip_out_assigned_argument(&argc,argv,"recover"); strip_out_standard_options(&argc,argv,show_help,show_version); if( argc != 2 ) { show_help(stdout); exit(12); } if((gm=GeneModel_from_GeneModelParam(gmp)) == NULL ) { fatal("Could not build gene model"); } codon_score = make_PairBaseCodonModelScore(comp_prob); nonc_score = make_PairBaseModelScore(); splice5 = ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice5score); splice3 = ComplexSequenceEval_from_pwmDNAScore_splice(gm->splice3score); if((ifp = openfile(argv[1],"r")) == NULL ) { fatal("Could not open file %s",argv[1]); } al = read_fasta_SeqAlign(ifp); assert(al); assert(al->len == 2); assert(al->seq[0]->len > 0); assert(al->seq[1]->len > 0); /* write_fasta_SeqAlign(al,stdout);*/ pbs = new_PairBaseSeq_SeqAlign(al); if( read_packaln == NULL ) { cseq = ComplexSequence_from_PairBaseSeq(pbs,splice5,splice3); } start = make_start_PairBaseCodonModelScore(ct); stop = make_stop_PairBaseCodonModelScore(ct); /* show_PairBaseCodonModelScore(stop,ct,stdout); */ /* for(i=0;i<pbs->anchor->len;i++) { printf("%3d %c For %-6d %-6d %c Rev %-6d %-6d\n",i,pbs->anchor->seq[i], CSEQ_PAIR_5SS(cseq,i),CSEQ_PAIR_3SS(cseq,i), char_complement_base(pbs->anchor->seq[i]), CSEQ_REV_PAIR_5SS(cseq,i),CSEQ_REV_PAIR_3SS(cseq,i)); } */ /* show_ComplexSequence(cseq,stdout); */ exonscore = SyExonScore_flat_model(100,150,0.1,1.0); /* for(i=0;i<cseq->length;i++) { fprintf(stdout,"%d PairSeq is %d score %d\n",i,CSEQ_PAIR_PAIRBASE(cseq,i),nonc_score->base[CSEQ_PAIR_PAIRBASE(cseq,i)]); } exit(0); */ if( read_packaln != NULL ) { packifp = openfile(read_packaln,"r"); if( packifp == NULL ) { fatal("File %s is unopenable - ignoring dump command",dump_packaln); } else { pal = read_simple_PackAln(packifp); } } else { pal = PackAln_bestmemory_SyWise20(exonscore,cseq,codon_score,nonc_score,start,stop,Probability2Score(1.0/100.0),Probability2Score(1.0/10000.0),Probability2Score(1.0/10.0),NULL,dpri); } alb = convert_PackAln_to_AlnBlock_SyWise20(pal); if( dump_packaln != NULL ) { packifp = openfile(dump_packaln,"w"); if( packifp == NULL ) { warn("File %s is unopenable - ignoring dump command",dump_packaln); } else { show_simple_PackAln(pal,packifp); } } show_score_sequence(alb,pbs,nonc_score,stdout); /* show_StandardOutputOptions(std_opt,alb,pal,"//",stdout); */ genomic = Genomic_from_Sequence(al->seq[0]); gr = new_GenomicRegion(genomic); gr2 = new_GenomicRegion(genomic); add_Genes_to_GenomicRegion_new(gr,alb); show_GenomicRegionOptions(sgro,gr,ct,"//",stdout); return 0; }
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); } } }