int main(int argc,char ** argv) { SequenceDB * db; Sequence * seq; SeqLookupInterface * sli; SeqLookupPos * slp; HSPScanInterface * hsi; LinearHSPmanager * lm; HitList * hl; CompMat * mat; int ret; HSPScanInterfacePara p; p.min_score= 30; p.max_results = 200; db = single_fasta_SequenceDB(argv[1]); mat = read_Blast_file_CompMat("blosum62.bla"); sli = new_ghash_SeqLookupInterface(); for(seq = init_SequenceDB(db,&ret); seq != NULL;seq = get_next_SequenceDB(db) ) { load_aa_flat_Sequence_SeqLookupInterface(sli,hard_link_Sequence(seq)); } seq = read_fasta_file_Sequence(argv[2]); assert(seq); hsi = Wise2_new_one_off_HSPScanInterface(sli,mat,20,10); /* hspm = simple_HSPScan_scan_query((void*)hsi->data,seq); */ lm = (*hsi->scan_query)(hsi->data,seq,&p); hl = Wise2_HitList_from_LinearHSPmanager(lm); Wise2_write_pseudoblast_HitList(hl,stdout); }
boolean build_objects(void) { boolean ret = TRUE; Protein * pro_temp; Genomic * gen_temp; FILE * ifp; startend = threestatemodel_mode_from_string(startend_string); if( startend == TSM_unknown ) { warn("String %s was unable to converted into a start/end policy\n",startend_string); ret = FALSE; } if( tstart_str != NULL ) { if( is_integer_string(tstart_str,&tstart) == FALSE || tstart < 0) { warn("Could not make %s out as target start",tstart); ret = FALSE; } } if( tend_str != NULL ) { if( is_integer_string(tend_str,&tend) == FALSE || tend < 0) { warn("Could not make %s out as target end",tend); ret = FALSE; } } if( is_integer_string(gap_str,&gap) == FALSE ) { warn("Could not make %s out as gap penalty (must be integer at the moment)",gap_str); ret = FALSE; } if( is_integer_string(ext_str,&ext) == FALSE ) { warn("Could not make %s out as gap penalty (must be integer at the moment)",ext_str); ret = FALSE; } if( is_embl == FALSE ) { if( (gen = read_fasta_file_Genomic(dna_seq_file,length_of_N)) == NULL ) { ret = FALSE; warn("Could not read genomic sequence in %s",dna_seq_file); gen = NULL; } } else { embl = read_EMBL_GenomicRegion_file(dna_seq_file); if( embl == NULL ) { warn("Could not read genomic EMBL file in %s",dna_seq_file); gen = NULL; ret = FALSE; } else { gen = hard_link_Genomic(embl->genomic); } } if( gen != NULL ) { if( tstart != -1 || tend != -1 ) { if( tstart == -1 ) tstart = 0; if( tend == -1 ) tend = gen->baseseq->len; gen_temp = truncate_Genomic(gen,tstart-1,tend); if( gen_temp == NULL ){ ret = FALSE; } else { free_Genomic(gen); gen = gen_temp; } } else { /* no truncation required */ } if( reverse == TRUE ) { if( tstart > tend ) { warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend); } gen_temp = reverse_complement_Genomic(gen); free_Genomic(gen); gen = gen_temp; } } /* * Can't truncate on GenomicRegion (for good reasons!). * but we want only a section of the EMBL file to be used * * So... swap genomic now. Positions in EMBL are still valid, * however - some genes will loose their sequence, which will be damaging. ;) */ if( is_embl ) { free_Genomic(embl->genomic); embl->genomic = hard_link_Genomic(gen); /* pointer could be dead anyway ;) */ } if( target_abs == TRUE ) { if( is_embl == TRUE ) { warn("Sorry you can't both use absolute positioning and EMBL files as I can't cope with all the coordinate remapping. You'll have to convert to fasta."); ret = FALSE; } gen->baseseq->offset = 1; gen->baseseq->end = strlen(gen->baseseq->seq); } if( alg_str != NULL ) { alg = gwrap_alg_type_from_string(alg_str); } else { if( use_tsm == TRUE ) { alg_str = "623L"; } else { alg_str = "623"; } alg = gwrap_alg_type_from_string(alg_str); } if( qstart_str != NULL ) { if( is_integer_string(qstart_str,&qstart) == FALSE || qstart < 0) { warn("Could not make %s out as query start",qstart); ret = FALSE; } } if( qend_str != NULL ) { if( is_integer_string(qend_str,&qend) == FALSE || qend < 0) { warn("Could not make %s out as query end",qend); ret = FALSE; } } if( use_tsm == FALSE ) { if( startend != TSM_default && startend != TSM_global && startend != TSM_local && startend != TSM_endbiased) { warn("Proteins can only have local/global/endbias startend policies set, not %s",startend_string); ret = FALSE; } if( (pro = read_fasta_file_Protein(protein_file)) == NULL ) { ret = FALSE; warn("Could not read Protein sequence in %s",protein_file); } else { if( qstart != -1 || qend != -1 ) { if( qstart == -1 ) qstart = 0; if( qend == -1 ) qend = pro->baseseq->len; pro_temp = truncate_Protein(pro,qstart-1,qend); if( pro_temp == NULL ){ ret = FALSE; } else { free_Protein(pro); pro = pro_temp; } } } } else { /** using a HMM **/ /*tsm = read_HMMer_1_7_ascii_file(hmm_file);*/ /*tsm = Wise2_read_ThreeStateModel_from_hmmer1_file(hmm_file);*/ tsm = HMMer2_read_ThreeStateModel(hmm_file); if( tsm == NULL ) { warn("Could not read hmm from %s\n",hmm_file); ret = FALSE; } else { display_char_in_ThreeStateModel(tsm); if( hmm_name != NULL ) { if( tsm->name != NULL ) ckfree(tsm->name); tsm->name = stringalloc(hmm_name); } if( tsm == NULL ) { warn("Could not read %s as a hmm",hmm_file); } /** have to set start/end **/ set_startend_policy_ThreeStateModel(tsm,startend,30,0.1); } } /* end of else tsm != NULL */ if( main_block_str != NULL ) { if( is_integer_string(main_block_str,&main_block) == FALSE ) { warn("Could not get maximum main_block number %s",main_block_str); ret = FALSE; } } if( is_double_string(subs_string,&subs_error) == FALSE ) { warn("Could not convert %s to a double",subs_error); ret = FALSE; } if( is_double_string(indel_string,&indel_error) == FALSE ) { warn("Could not convert %s to a double",indel_error); ret = FALSE; } if( is_double_string(allN_string,&allN) == FALSE ) { warn("Could not convert %s to a double",allN_string); ret = FALSE; } if( strcmp(cfreq_string,"model") == 0 ) { model_codon = TRUE; } else if ( strcmp(cfreq_string,"flat") == 0 ) { model_codon = FALSE; } else { warn("Cannot interpret [%s] as a codon modelling parameter\n",cfreq_string); ret = FALSE; } if( strcmp(splice_string,"model") == 0 ) { model_splice = TRUE; } else if ( strcmp(splice_string,"flat") == 0 ) { model_splice = FALSE; gmp->use_gtag_splice = TRUE; } else { warn("Cannot interpret [%s] as a splice modelling parameter\n",splice_string); ret = FALSE; } if( strcmp(null_string,"syn") == 0 ) { use_syn = TRUE; } else if ( strcmp(null_string,"flat") == 0 ) { use_syn = FALSE; } else { warn("Cannot interpret [%s] as a null model string\n",null_string); ret = FALSE; } if( strcmp(intron_string,"model") == 0 ) { use_tied_model = FALSE; } else if ( strcmp(intron_string,"tied") == 0 ) { use_tied_model = TRUE; } else { warn("Cannot interpret [%s] as a intron tieing switch\n",intron_string); ret = FALSE; } if( (rm = default_RandomModel()) == NULL) { warn("Could not make default random model\n"); ret = FALSE; } if( use_new_stats == 0 ) { if( (gf = read_GeneFrequency21_file(gene_file)) == NULL) { ret = FALSE; warn("Could not read a GeneFrequency file in %s",gene_file); } } else { if( (gs = GeneStats_from_GeneModelParam(gmp)) == NULL ){ ret=FALSE; warn("Could not read gene statistics in %s",new_gene_file); } } /* end of else using new gene stats */ if( (mat = read_Blast_file_CompMat(matrix_file)) == NULL) { if( use_tsm == TRUE ) { info("I could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.",matrix_file); } else { warn("Could not read Comparison matrix file in %s",matrix_file); ret = FALSE; } } if( (ct = read_CodonTable_file(codon_file)) == NULL) { ret = FALSE; warn("Could not read codon table file in %s",codon_file); } if( (ofp = openfile(output_file,"W")) == NULL) { warn("Could not open %s as an output file",output_file); ret = FALSE; } rmd = RandomModelDNA_std(); return ret; }
boolean build_objects(void) { boolean ret = TRUE; Protein * pro_temp; SequenceDB * psdb; startend = threestatemodel_mode_from_string(startend_string); if( startend == TSM_unknown ) { warn("String %s was unable to converted into a start/end policy\n",startend_string); ret = FALSE; } if( use_single_dna == TRUE ) { cdna = read_fasta_file_cDNA(dna_seq_file); if( cdna == NULL ) { warn("Could not open single dna sequence in %s",dna_seq_file); ret = FALSE; } } else { sdb = single_fasta_SequenceDB(dna_seq_file); if( sdb == NULL ) { warn("Could not build a sequence database on %s",dna_seq_file); ret = FALSE; } } rm = default_RandomModel(); if( (mat = read_Blast_file_CompMat(matrix_file)) == NULL) { if( use_tsm == TRUE ) { info("I could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.",matrix_file); } else { warn("Could not read Comparison matrix file in %s",matrix_file); ret = FALSE; } } if( is_integer_string(gap_str,&gap) == FALSE ) { warn("Could not get gap string number %s",gap_str); ret = FALSE; } if( is_integer_string(ext_str,&ext) == FALSE ) { warn("Could not get ext string number %s",ext_str); ret = FALSE; } if( qstart_str != NULL ) { if( is_integer_string(qstart_str,&qstart) == FALSE || qstart < 0) { warn("Could not make %s out as query start",qstart); ret = FALSE; } } if( qend_str != NULL ) { if( is_integer_string(qend_str,&qend) == FALSE || qend < 0) { warn("Could not make %s out as query end",qend); ret = FALSE; } } if( aln_number_str != NULL ) { if( is_integer_string(aln_number_str,&aln_number) == FALSE || aln_number < 0) { warn("Weird aln number string %s...\n",aln_number_str); ret = FALSE; } } if( report_str != NULL ) { if( is_integer_string(report_str,&report_stagger) == FALSE ) { warn("Weird report stagger asked for %s",report_str); ret = FALSE; } } if( use_pfam1 == TRUE ) { tsmdb = new_PfamHmmer1DB_ThreeStateDB(protein_file); if( set_search_type_ThreeStateDB(tsmdb,startend_string) == FALSE) { warn("Unable to set global/local switch on threestatedb"); ret = FALSE; } } else if ( use_pfam2 == TRUE ) { tsmdb = HMMer2_ThreeStateDB(protein_file); if( set_search_type_ThreeStateDB(tsmdb,startend_string) == FALSE) { warn("Unable to set global/local switch on threestatedb"); ret = FALSE; } } else if ( use_tsm == TRUE) { /** using a HMM **/ tsm = HMMer2_read_ThreeStateModel(protein_file); if( tsm == NULL ) { warn("Could not read hmm from %s\n",protein_file); ret = FALSE; } else { display_char_in_ThreeStateModel(tsm); if( hmm_name != NULL ) { if( tsm->name != NULL ) ckfree(tsm->name); tsm->name = stringalloc(hmm_name); } else { if( tsm->name == NULL ) { tsm->name = stringalloc(protein_file); } } /** have to set start/end **/ set_startend_policy_ThreeStateModel(tsm,startend,15,0.2); tsmdb = new_single_ThreeStateDB(tsm,rm); if( tsmdb == NULL ) { warn("Could not build a threestatemodel database from a single tsm. Weird!"); ret = FALSE; } } /* end of else tsm != NULL */ } /* end of else is tsm */ else if( use_single_pro ) { if( startend != TSM_default && startend != TSM_global && startend != TSM_local ) { warn("Proteins can only have local/global startend policies set, not %s",startend_string); ret = FALSE; } if( (pro = read_fasta_file_Protein(protein_file)) == NULL ) { ret = FALSE; warn("Could not read Protein sequence in %s",protein_file); } else { if( qstart != -1 || qend != -1 ) { if( qstart == -1 ) qstart = 0; if( qend == -1 ) qend = pro->baseseq->len; pro_temp = truncate_Protein(pro,qstart-1,qend); if( pro_temp == NULL ){ ret = FALSE; } else { free_Protein(pro); pro = pro_temp; } } if( startend == TSM_global) tsm = global_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,-gap,-ext); else tsm = ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,-gap,-ext); if( tsm == NULL ) { warn("Could not build ThreeStateModel from a single protein sequence..."); ret = FALSE; } else { tsmdb = new_single_ThreeStateDB(tsm,rm); if( tsmdb == NULL ) { warn("Could not build a threestatemodel database from a single tsm. Weird!"); ret = FALSE; } } /* end of could build a TSM */ } /* else is a real protein */ } /* end of else is single protein */ else if (use_db_pro == TRUE ) { psdb = single_fasta_SequenceDB(protein_file); tsmdb = new_proteindb_ThreeStateDB(psdb,mat,-gap,-ext); free_SequenceDB(psdb); } else { warn("No protein input file! Yikes!"); } /*** if( use_tsm == FALSE ) { } else { ****/ if( main_block_str != NULL ) { if( is_integer_string(main_block_str,&main_block) == FALSE ) { warn("Could not get maximum main_block number %s",main_block_str); ret = FALSE; } } if( evalue_search_str != NULL && is_double_string(evalue_search_str,&evalue_search_cutoff) == FALSE ) { warn("Could not convert %s to a double",evalue_search_str); ret = FALSE; } if( is_double_string(search_cutoff_str,&search_cutoff) == FALSE ) { warn("Could not convert %s to a double",search_cutoff_str); ret = FALSE; } if( is_double_string(subs_string,&subs_error) == FALSE ) { warn("Could not convert %s to a double",subs_error); ret = FALSE; } if( is_double_string(indel_string,&indel_error) == FALSE ) { warn("Could not convert %s to a double",indel_error); ret = FALSE; } if( is_double_string(allN_string,&allN) == FALSE ) { warn("Could not convert %s to a double",allN_string); ret = FALSE; } if( strcmp(null_string,"syn") == 0 ) { use_syn = TRUE; } else if ( strcmp(null_string,"flat") == 0 ) { use_syn = FALSE; } else { warn("Cannot interpret [%s] as a null model string\n",null_string); ret = FALSE; } if( alg_str != NULL ) { alg = alg_estwrap_from_string(alg_str); } else { alg_str = "312"; alg = alg_estwrap_from_string(alg_str); } if( aln_alg_str != NULL ) { aln_alg = alg_estwrap_from_string(aln_alg_str); } else { /* if it is a protein, don't loop */ if( use_single_pro == TRUE || use_db_pro == TRUE ) aln_alg_str = "333"; else aln_alg_str = "333L"; aln_alg = alg_estwrap_from_string(aln_alg_str); } if( (rm = default_RandomModel()) == NULL) { warn("Could not make default random model\n"); ret = FALSE; } if( (ct = read_CodonTable_file(codon_file)) == NULL) { ret = FALSE; warn("Could not read codon table file in %s",codon_file); } if( (ofp = openfile(output_file,"W")) == NULL) { warn("Could not open %s as an output file",output_file); ret = FALSE; } rmd = RandomModelDNA_std(); cps = flat_cDNAParser(indel_error); cm = flat_CodonMapper(ct); sprinkle_errors_over_CodonMapper(cm,subs_error); return ret; }
HSPScanInterface * new_HSPScanInterface_from_ScanWiseHSPImpl(ScanWiseHSPImpl * i,ProteinIndexConstructor * pic,SeqLookupLoadPara * slp) { HSPScanInterface * out; SeqLookupInterface * sli; SequenceDB * db; Sequence * seq; CompMat * mat; int ret; int c; mat = read_Blast_file_CompMat(i->matrix_file); if( i->use_corba == FALSE && i->use_mysql == FALSE && i->use_wiseserver == FALSE && i->use_compress == FALSE && i->use_multiscan == FALSE) { if( i->direct_sequence == NULL ) { fatal("If no server based sequence, must have direct sequence"); } else { db = single_fasta_SequenceDB(i->direct_sequence); sli = new_SeqLookupInterface_from_ProteinIndexConstructor(pic); load_SequenceDB_SeqLookupLoadPara(slp,db,sli); free_SequenceDB(db); out = new_one_off_HSPScanInterface(sli,mat,15,40); } } else if( i->use_corba == TRUE ) { #ifdef SCAN_CORBA if( i->ior_file == NULL ) { fatal("Corba specified, but no ior file given"); } out = new_corba_HSPScan(sorb,i->ior_file,mat); #else fatal("Asking for CORBA, but scanwisep was not compiled with SCAN_CORBA defined."); #endif } else if ( i->use_mysql == TRUE ) { #ifdef SCAN_MYSQL out = new_HSPScanInterface_MysqlProteinIndex(i->host,i->dbname,i->username,i->password,mat,i->step); #else fatal("Asking for mysql, but scanwisep was not compiled with SCAN_MYSQL defined"); #endif } else if ( i->use_wiseserver == TRUE ) { #ifdef SCAN_WISESERVER out = new_wise_transfer_HSPScanInterface(i->host,i->port); #else fatal("Asking for wiseserver, but scanwisep was not compiled with SCAN_WISESERVER defined"); #endif } else if ( i->use_compress == TRUE ) { #ifdef SCAN_COMPRESS sli = new_direct_CompressedProteinLookup(); db = single_fasta_SequenceDB(i->direct_sequence); load_SequenceDB_SeqLookupLoadPara(slp,db,sli); free_SequenceDB(db); out = new_one_off_HSPScanInterface(sli,mat,15,40); #else fatal("Asking for compressed, but scanwisep was not compiled with SCAN_COMPRESS defined"); #endif } else if( i->use_multiscan == TRUE ) { if( i->multiscan_file == NULL ) { fatal("Must provide a file for a multiple server scan"); } out = new_multiclient_HSPScanInterface(i->multiscan_file); } assert(out != NULL); free_CompMat(mat); /* hard linked internally */ return out; }
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) { 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); } } }
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; }