void show_StandardOutputOptions(StandardOutputOptions * out,AlnBlock * alb,PackAln * pal,char * divide_str,FILE * ofp) { assert(out); assert(alb); assert(pal); assert(ofp); assert(divide_str); if( out->show_alb == TRUE ) { mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp); fprintf(ofp,"%s\n",divide_str); } if( out->show_cumlative_alb == TRUE ) { mapped_ascii_AlnBlock(alb,Score2Bits,1,ofp); fprintf(ofp,"%s\n",divide_str); } if( out->show_cumlative_pal == TRUE ) { show_bits_and_cumlative_PackAln(pal,ofp); fprintf(ofp,"%s\n",divide_str); } if( out->show_pal == TRUE ) { show_simple_PackAln(pal,ofp); fprintf(ofp,"%s\n",divide_str); } return; }
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 * 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,k; ThreeStateModel * temptsm; AlnBlock * alb; PackAln * pal; MatchSummarySet * mss; Protein * ps; cDNA * cdna; double bits; boolean fitted_res = FALSE; AlnBlockList * alist; AlnBlock * anchored; SequenceSet * set; AlnColumn * alt; Protein * trans; /* sort by bit score first */ sort_Hscore_by_score(hs); if( search_mode == PC_SEARCH_S2DB ) { if( hs->his == NULL || hs->his->total < 1000 ) { info("Cannot fit histogram to a db smaller than 1,000"); fprintf(ofp,"[Warning: Can't fit histogram to a db smaller than 1,000]\n\n"); show_histogram = FALSE; } else { fitted_res = TRUE; fit_Hscore_to_EVD(hs,20); } } /* deal with initialising anchored alignment. * Could be done for either single HMMs or single proteins, * but we will only do it for HMMs at the moment */ if( make_anchored_aln == TRUE ) { if( tsm == NULL ) { warn("Attempting to make an achored alignment without a HMM. impossible!"); make_anchored_aln = FALSE; } else { anchored = single_unit_AlnBlock(tsm->len,"MATCH_STATE"); set = SequenceSet_alloc_std(); } } /* dofus catcher */ if( aln_alg != alg ) { fprintf(ofp,"\n#\n#WARNING!\n#\n# Your alignment algorithm is different from your search algorithm.\n# This is probably quite sensible but will lead to differing scores.\n# Use the search score as an indicator of the significance of the match\n# Read the docs for more information\n#\n"); } fprintf(ofp,"\n\n#High Score list\n"); fprintf(ofp,"#Protein ID DNA Str ID Bits Evalue\n"); fprintf(ofp,"--------------------------------------------------------------------------\n"); for(i=0;i<hs->len;i++) { bits = Score2Bits(hs->ds[i]->score); if( bits < search_cutoff ) { break; } if( fitted_res == TRUE && evalue_search_str != NULL ) { if( hs->ds[i]->evalue > evalue_search_cutoff ) break; } if( fitted_res == TRUE) fprintf(ofp,"Protein %-20sDNA [%c] %-24s %.2f %.2g\n",hs->ds[i]->query->name,hs->ds[i]->target->is_reversed == TRUE ? '-' : '+',hs->ds[i]->target->name,bits,hs->ds[i]->evalue); else fprintf(ofp,"Protein %-20sDNA [%c] %-24s %.2f\n",hs->ds[i]->query->name,hs->ds[i]->target->is_reversed == TRUE ? '-' : '+',hs->ds[i]->target->name,bits); } if( search_mode == PC_SEARCH_S2DB && show_histogram == TRUE ) { fprintf(ofp,"\n\n#Histogram\n"); fprintf(ofp,"-----------------------------------------------------------------------\n"); PrintASCIIHistogram(hs->his,ofp); } fprintf(ofp,"\n\n#Alignments\n"); fprintf(ofp,"-----------------------------------------------------------------------\n"); for(i=0;i<hs->len;i++) { bits = Score2Bits(hs->ds[i]->score); if( bits < search_cutoff ) { break; } if( i >= aln_number ) { break; } if( fitted_res == TRUE && evalue_search_str != NULL ) { if( hs->ds[i]->evalue > evalue_search_cutoff ) break; } fprintf(ofp,"\n\n>Results for %s vs %s (%s) [%d]\n",hs->ds[i]->query->name,hs->ds[i]->target->name,hs->ds[i]->target->is_reversed == TRUE ? "reverse" : "forward",i+1 ); cdna = get_cDNA_from_cDNADB(cdb,hs->ds[i]->target); temptsm = indexed_ThreeStateModel_ThreeStateDB(tsmdb,hs->ds[i]->query); alb = AlnBlock_from_TSM_estwise_wrap(temptsm,cdna,cps,cm,ct,rmd,aln_alg,use_syn,allN,flat_insert,dpri,&pal); if( alb == NULL ) { warn("Got a NULL alignment. Exiting now due to presumed problems"); fprintf(ofp,"\n\n*Got a NULL alignment. Exiting now due to presumed problems*\n\n"); return FALSE; } if( use_single_pro == FALSE) mss = MatchSummarySet_from_AlnBlock_genewise(alb,temptsm->name,1,cdna->baseseq); else mss = MatchSummarySet_from_AlnBlock_genewise(alb,pro->baseseq->name,pro->baseseq->offset,cdna->baseseq); if( show_pretty == TRUE ) { fprintf(ofp,"\n%s output\nScore %4.2f bits over entire alignment.\nThis will be different from per-alignment scores. See manual for details\nFor computer parsable output, try %s -help or read the manual\n",program_name,Score2Bits(pal->score),program_name); if( use_syn == FALSE ) { fprintf(ofp,"Scores as bits over a flat simple random model\n\n"); } else { fprintf(ofp,"Scores as bits over a synchronous coding model\n\n"); } ps = pseudo_Protein_from_ThreeStateModel(temptsm); protcdna_ascii_display(alb,ps->baseseq->seq,ps->baseseq->name,ps->baseseq->offset,cdna,ct,15,main_block,TRUE,ofp); free_Protein(ps); fprintf(ofp,"%s\n",divide_str); } if( show_match_sum == TRUE ) { show_MatchSummary_genewise_header(ofp); show_MatchSummarySet_genewise(mss,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_pep == TRUE ) { alt = alb->start; for(;alt != NULL;) { trans = Protein_from_GeneWise_AlnColumn(cdna->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_AlnBlock == TRUE ) { mapped_ascii_AlnBlock(alb,Score2Bits,0,ofp); fprintf(ofp,"%s\n",divide_str); } if( show_PackAln == TRUE ) { show_simple_PackAln(pal,ofp); fprintf(ofp,"%s\n",divide_str); } /* * This goes at the end because it destroys the alb structure */ if( make_anchored_aln == TRUE ) { /* attach sequence to als in alb, so we have it for later use */ alb->seq[1]->data = (void *) cdna->baseseq; /* add to SequenceSet so we can destroy the memory */ add_SequenceSet(set,hard_link_Sequence(cdna->baseseq)); alist = split_AlnBlock(alb,is_random_AlnColumn_genewise); for(k=0;k<alist->len;k++) { /* actually produce the anchored alignment */ /*mapped_ascii_AlnBlock(alist->alb[k],Score2Bits,stderr);*/ add_to_anchored_AlnBlock(anchored,alist->alb[k]); /* dump_ascii_AlnBlock(anchored,stderr);*/ } } alb = free_AlnBlock(alb); pal = free_PackAln(pal); mss = free_MatchSummarySet(mss); cdna = free_cDNA(cdna); temptsm = free_ThreeStateModel(temptsm); } if( do_complete_analysis == TRUE ) { fprintf(ofp,"\n\n#Complete Analysis\n"); fprintf(ofp,"-------------------------------------------------------------\n\n"); /* ok - end of loop over relevant hits. If we have an * anchored alignment, print it out! */ if( make_anchored_aln == TRUE ) { /*dump_ascii_AlnBlock(anchored,stderr);*/ write_mul_estwise_AlnBlock(anchored,ct,ofp); fprintf(ofp,"%s\n",divide_str); } } return TRUE; }
int main (int argc,char ** argv) { MappedCloneSet * trusted; MappedCloneSet * weak; MappedCloneMatch * match; FILE * in; int kbyte = 10000; PackAln * pal; AlnBlock * alb; int spread = 30; boolean show_alb = 0; boolean show_pal = 0; boolean show_zip = 1; boolean show_path = 0; char * alg_string = "local"; char * temp; char * divide_string = "//"; 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,"zip",&show_zip); strip_out_boolean_def_argument(&argc,argv,"path",&show_path); strip_out_integer_argument(&argc,argv,"wgap",&query_gap_start); strip_out_integer_argument(&argc,argv,"wext",&query_gap_extend); strip_out_integer_argument(&argc,argv,"wswitch",&query_switch_cost); strip_out_integer_argument(&argc,argv,"tgap",&target_gap_start); strip_out_integer_argument(&argc,argv,"text",&target_gap_extend); strip_out_integer_argument(&argc,argv,"match",&match_score); strip_out_integer_argument(&argc,argv,"mismatch",&mismatch_score); temp =strip_out_assigned_argument(&argc,argv,"alg"); if( temp != NULL ) { alg_string = temp; } strip_out_integer_argument(&argc,argv,"spread",&spread); strip_out_integer_argument(&argc,argv,"kbyte",&kbyte); strip_out_standard_options(&argc,argv,show_help,show_version); if( argc != 3 ) { show_help(stdout); exit(12); } in = fopen(argv[1],"r"); if( in == NULL ) { fatal("Unable to open %s",argv[1]); } trusted = read_MappedCloneSet(in); /* fprintf(stderr,"first start %d\n",trusted->clone[0]->start);*/ in = fopen(argv[2],"r"); if( in == NULL ) { fatal("Unable to open %s",argv[2]); } change_max_BaseMatrix_kbytes(kbyte); weak = read_MappedCloneSet(in); synchronise_MappedCloneSets(trusted,weak); /* fprintf(stderr,"score for 2,2 is %d\n",MappedCloneSet_match(weak,trusted,2,2,0,10,-5)); */ match = new_MappedCloneMatch(weak,trusted,match_score,mismatch_score); fprintf(stderr,"Match matrix calculated\n"); if( strcmp(alg_string,"global") == 0 ) { pal = PackAln_bestmemory_CloneWise(weak,trusted,match,-query_gap_start,-query_gap_extend,-target_gap_start,-target_gap_extend,spread,-query_switch_cost,NULL); alb = convert_PackAln_to_AlnBlock_CloneWise(pal); } else if ( strcmp(alg_string,"local") == 0 ) { pal = PackAln_bestmemory_LocalCloneWise(weak,trusted,match,-query_gap_start,-query_gap_extend,-target_gap_start,-target_gap_extend,spread,-query_switch_cost,NULL); alb = convert_PackAln_to_AlnBlock_LocalCloneWise(pal); } else { /* keep gcc happy */ pal = NULL; alb = NULL; fatal("Not a proper algorithm string %s",alg_string); } if( show_path ) { extended_path(alb,weak,trusted,stdout); fprintf(stdout,"%s\n",divide_string); } if( show_zip ) { debug_zip(alb,weak,trusted,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_pal ) { show_simple_PackAln(pal,stdout); fprintf(stdout,"%s\n",divide_string); } return 0; }
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 * query; Sequence * target; ComplexSequence * query_cs; ComplexSequence * target_cs; ComplexSequenceEvalSet * evalfunc; CompMat * comp; char * comp_file; int gap = (12); int ext = (2); boolean show_raw_output = FALSE; boolean show_label_output = FALSE; boolean show_fancy_output = FALSE; boolean has_outputted = FALSE; PackAln * pal; AlnBlock * alb; /* * 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) * -r - raw matrix output * -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); } show_raw_output = strip_out_boolean_argument(&argc,argv,"r"); 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_raw_output == FALSE && 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); 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); } /* * Convert sequences to ComplexSequences: * To do this we need an protein ComplexSequenceEvalSet * */ evalfunc = default_aminoacid_ComplexSequenceEvalSet(); query_cs = new_ComplexSequence(query,evalfunc); if( query_cs == NULL ) { fatal("Unable to make a protein complex sequence from %s",query->name); } target_cs = new_ComplexSequence(target,evalfunc); if( target_cs == NULL ) { fatal("Unable to make a protein complex sequence from %s",target->name); } /* * Make an alignment. I don't care about the implementation: * If the sequences are small enough then it should use explicit memory. * Long sequences should use divide and conquor methods. * * Calling PackAln_bestmemory_ProteinSW is the answer * This function decides on the best method considering the * memory and changes accordingly. It frees the matrix memory * at the end as well. * */ pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp,-gap,-ext,NULL); if( pal == NULL ) { fatal("Unable to make an alignment from %s and %s",query->name,target->name); } /* * ok, make other alignment forms, and be ready to show */ alb = convert_PackAln_to_AlnBlock_ProteinSW(pal); /* * show output. If multiple outputs, divide using // */ if( show_raw_output == TRUE ) { show_simple_PackAln(pal,stdout); puts("//\n"); } if( show_label_output == TRUE ) { show_flat_AlnBlock(alb,stdout); } 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_ComplexSequence(query_cs); free_ComplexSequence(target_cs); free_PackAln(pal); free_AlnBlock(alb); return 0; }