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; }
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); } } }