binaries/src/tcoffee/t_coffee_source/util_lib/reformat.h

   1 /******************************COPYRIGHT NOTICE*******************************/
   2 /*  (c) Centro de Regulacio Genomica                                                        */
   3 /*  and                                                                                     */
   4 /*  Cedric Notredame                                                                        */
   5 /*  12 Aug 2014 - 22:07.                                                                    */
   6 /*All rights reserved.                                                                      */
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  14 /*    T-COFFEE is distributed in the hope that it will be useful,                           */
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  24 /*  cedric.notredame@europe.com                                                             */
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  26 /******************************COPYRIGHT NOTICE*******************************/
  27 #ifndef __REFORMAT_H
  28 #define __REFORMAT_H
  29
  30 typedef struct
  31     {
  32       Alignment *A;
  33       Weights *W;
  34       Sequence *S;
  35       int **M;
  36       Structure *RNA_ST;
  37       NT_node T;
  38       Constraint_list *CL;
  39       char format[100];
  40       char file[100];
  41       int rm_gap;
  42
  43 }Sequence_data_struc;
  44
  45 typedef struct
  46     {
  47         char **symbol_list;
  48         int n_symbol;
  49         char *coor_file;
  50         int rm_gap;
  51         int keep_case;
  52         int keep_name;
  53         int use_consensus;
  54 }Action_data_struc;
  55
  56 /*Control of alignment sizes*/
  57 int  set_landscape_msa (int len);
  58 int get_msa_line_length (int line, int aln_len);
  59
  60 int seq_reformat (int argc, char **argv);
  61
  62 Sequence_data_struc *read_data_structure ( char *in_format, char *in_file,Action_data_struc *RAD);
  63 Alignment * read_fasta_aln_noceck ( char *name, Alignment *A);
  64 Alignment * main_read_aln ( char *name, Alignment *A);
  65 Sequence  * read_sequences ( char *name);
  66 Sequence  * read_alifold   ( char *name);
  67 Alignment *alifold2aln     ( char *name);
  68 Sequence  * main_read_seq ( char *mname);
  69 int output_format_aln ( char *format, Alignment *A, Alignment *EA,char *name);
  70 int main_output   ( Sequence_data_struc *D1, Sequence_data_struc *D2, Sequence_data_struc *DST, char *out_format, char *out_file);
  71
  72 char * identify_seq_format ( char *file);
  73 char * name2type_name ( char *name);
  74 char identify_format (char **fname);
  75 char **identify_list_format ( char **list, int n);
  76
  77 int type_is_exon_boundaries(char **seq, int n);
  78
  79 int format_is_oligo  ( char *file);
  80 int format_is_msf  ( char *file);
  81 int format_is_fasta( char *file);
  82 // int format_is_fasta_aln( char *file);
  83 int format_is_fasta_aln ( char *file, int i_know_that_it_not_seq);
  84 int format_is_fasta_seq( char *file);
  85 int is_pir_name (char *name);
  86 int format_is_pir  ( char *file);
  87 int format_is_pir_aln( char *file);
  88 int format_is_pir_seq( char *file);
  89 int pir_name (char *name);
  90 int format_is_conc_aln (char *file);
  91 int format_is_saga  ( char *file);
  92 int format_is_swissprot (char *name);
  93
  94 int is_seq ( char *name);
  95 int is_aln ( char *name);
  96 int has_pdb (char *name);
  97 int is_stockhom_aln ( char *name);
  98 int is_blast_file (char *name);
  99 int is_sap_file (char *name);
 100 int is_pdb_file ( char *name);
 101 int is_simple_pdb_file ( char *name);
 102 char *fix_pdb_file (char *name);
 103
 104 int is_pdb_name ( char *name);
 105 char* get_pdb_id(char *name);
 106 char* get_pdb_struc(char *name, int start, int end);
 107 char*  seq_is_pdb_struc ( Sequence *S, int i);
 108 char* is_pdb_struc ( char *name); /*Returns NULL if not a PDB structure Or a the name of a file containing a PDB structure*/
 109 int is_matrix (char *name);
 110
 111 int is_lib (char *name);
 112 int is_lib_01 (char *name);
 113 int is_lib_02 (char *name);
 114 int is_lib_list ( char *name);
 115 int is_single_seq_weight_file (char *fname);
 116 int is_treelist(char *name);
 117 int is_newick  (char *name);
 118 int is_nexus (char *file);
 119
 120 int is_method ( char *file);
 121
 122 char *format_name2aln_format_name (char *name);
 123 int is_in_format_list ( char *name);
 124 int is_out_format_list ( char *name);
 125 int is_struc_in_format_list ( char *name);
 126 int is_struc_out_format_list ( char *name);
 127 /*******************************************************************************************/
 128 /*                                                                                         */
 129 /*                                                                                         */
 130 /*                               INPUT MISC                                               */
 131 /*                                                                                         */
 132 /***************************************************************************************** */
 133
 134 char *** read_rename_file ( char *fname, int mode);
 135 void get_barton_list_tc_seq ( char *in_file);
 136 int process_barton_entry (char *buf, char *name);
 137
 138 Structure *read_rna_struc_number ( Alignment *A, char *fname);
 139 char ** read_lib_list (char *name, int *n);
 140 /*******************************************************************************************/
 141 /*                                                                                         */
 142 /*                                                                                         */
 143 /*                               INPUT WEIGHTS                                             */
 144 /*                                                                                         */
 145 /***************************************************************************************** */
 146 Weights* get_amps_sd_scores ( char *fname);
 147 Weights *read_seq_weight (char **name, int nseq, char* seq_weight);
 148 /*******************************************************************************************/
 149 /*                                                                                         */
 150 /*                                                                                         */
 151 /*                               INPUT SEQUENCES                                            */
 152 /*                                                                                         */
 153 /***************************************************************************************** */
 154 char ***read_group ( char *file);
 155 Sequence* get_pdb_sequence           ( char *fname);
 156 Sequence* get_struc_gor              ( char *fname);
 157 Sequence* get_dialign_sequence       ( char *fname);
 158 Sequence* get_pima_sequence          ( char *fname);
 159 Sequence* get_sequence_dali          ( char *fname);
 160 Sequence* get_pir_sequence           ( char *fname, char *comment_name);
 161 Sequence* perl_reformat2fasta        ( char *perl_script, char *file);
 162
 163 Sequence* get_fasta_sequence         ( char *fname, char *comment_name);
 164 Sequence* get_fasta_sequence_num     ( char *fname, char *comment_name);
 165 Sequence* get_fasta_sequence_raw     ( char *fname, char *comment_name);
 166 Sequence *get_file_list ( char *fname);
 167 Sequence *get_tree_file_list ( char *fname);
 168
 169 Sequence* get_gor_sequence           ( char *fname, char *comment_name);
 170 Sequence* get_swissprot_sequence     ( char *fname, char *comment_name);
 171 int  fscanf_seq_name ( FILE *fp, char *sname);
 172
 173 void read_check ( Alignment *A, char *check_file);
 174 void read_stockholm_aln ( char *fname, Alignment *A);
 175 void read_aln ( char *fname, Alignment *A);
 176 void read_number_aln ( char *fname, Alignment *A);
 177 Alignment *read_blast_aln  ( char *fname, Alignment *A);
 178 void read_msf_aln ( char *fname, Alignment *A);
 179 void read_amps_aln ( char *in_file, Alignment *A);
 180 int get_amps_seq_name ( char **name, char* fname);
 181 Alignment *read_gotoh_aln ( char *fname, Alignment *A);
 182
 183 void undump_msa ( Alignment *A, char *tmp);
 184 void dump_msa ( char *file,Alignment *A, int nseq, int *lseq);
 185 /*******************************************************************************************/
 186 /*                                                                                         */
 187 /*                                                                                         */
 188 /*                               OUTPUT MATRICES                                           */
 189 /*                                                                                         */
 190 /***************************************************************************************** */
 191 int output_freq_mat ( char *outfile, Alignment *A);
 192 /*******************************************************************************************/
 193 /*                                                                                         */
 194 /*                                                                                         */
 195 /*                               OUTPUT P-Values                                           */
 196 /*                                                                                         */
 197 /***************************************************************************************** */
 198 float output_maln_pval ( char *outfile, Alignment *A);
 199 /*******************************************************************************************/
 200 /*                                                                                         */
 201 /*                                                                                         */
 202 /*                               OUTPUT WEIGHTS                                            */
 203 /*                                                                                         */
 204 /***************************************************************************************** */
 205 void  output_similarities (char *file, Alignment *A, char *mode);
 206 void  output_similarities_pw (char *file, Alignment *A, Alignment *B, char *mode);
 207 Alignment * similarities_file2aln ( char *file);
 208 int** input_similarities (char *file, Alignment *A, char *mode);
 209
 210 void output_statistics (char *file, Alignment *A, char *mode);
 211 void output_pw_weights4saga ( Weights *W, float **w_list, char *wfile);
 212 int  output_seq_weights ( Weights *W, char *wfile);
 213 FILE * display_weights (Weights *W, FILE *fp);
 214 /*******************************************************************************************/
 215 /*                                                                                         */
 216 /*                                                                                         */
 217 /*                               OUTPUT SEQ                                                */
 218 /*                                                                                         */
 219 /***************************************************************************************** */
 220 char** clean_seq_names (char **names, int n, int mode);
 221 char *clean_seq_name (char *name, int mode);
 222
 223
 224 void output_pir_seq1 (char *fname, Alignment*A );
 225 void output_pir_seq (char *fname, Alignment*A );
 226 void output_gor_seq (char *fname, Alignment*A );
 227 void output_mult_fasta_seq (char *fname, Alignment*A, int n );
 228
 229 void main_output_fasta_seq ( char *fname, Alignment *A, int header);
 230 void output_fasta_simple   ( char *name, Sequence *S);
 231 void output_fasta_seqS (char *fname, Sequence *S );
 232 void output_fasta_seq1 (char *fname, Alignment*A );
 233 void output_fasta_seq2 (char *fname, Alignment*A );
 234 char *output_fasta_seqX (char *name, char *mode, Sequence *S, Alignment *A, int i);
 235
 236 void output_pir_check (char *fname,int nseq, char **A );
 237 void output_fasta_seq (char *fname, Alignment*A );
 238 void output_gotoh_seq (char *fname, Alignment*A );
 239 void output_est_prf   (char *fname, Alignment *A);
 240 void output_gor_seq (char *fname, Alignment*A );
 241 /*******************************************************************************************/
 242 /*                                                                                         */
 243 /*                                                                                         */
 244 /*                               OUTPUT ALN                                                */
 245 /*                                                                                         */
 246 /***************************************************************************************** */
 247 void output_pir_aln    ( char *fname,Alignment*A);
 248 void output_model_aln  ( char *fname,Alignment*A );
 249 char * output_fasta_sub_aln (char *fname, Alignment*A, int ns, int *ls  );
 250 char * output_fasta_sub_aln2 (char *fname, Alignment*A, int *ns, int **ls  );
 251
 252 void ouput_suchard_aln ( char *fname,Alignment*A);
 253 void output_fasta_aln  ( char *fname, Alignment *A);
 254 void output_mfasta_aln  ( char *fname, Alignment *A);
 255
 256 void output_xmfa_aln  ( char *fname, Alignment *A);
 257 void output_msf_aln    ( char *fname,Alignment*B);
 258 FILE * output_generic_interleaved_aln (FILE *fp, Alignment *B, int line, char gap, char *mode);
 259 void output_stockholm_aln (char *file, Alignment *A, Alignment *ST);
 260 void output_clustal_aln( char *name, Alignment*B);
 261 void output_strict_clustal_aln( char *name, Alignment*B);
 262 void output_generic_clustal_aln( char *name, Alignment*B, char *format);
 263 void output_saga_aln   ( char *name, Alignment*B);
 264 void output_rphylip_aln ( char *name, Alignment*B);
 265 void output_phylip_aln ( char *name, Alignment*B);
 266 void output_mocca_aln  ( char *name, Alignment*B,Alignment*S);
 267 void output_rnalign    (char *out_file, Alignment*A,Sequence *STRUC);
 268 void output_pw_lib_saga_aln (char *lib_name, Alignment *A );
 269 void output_lib        (char *lib_name, Alignment *A );
 270 void output_compact_aln( char *name, Alignment *B);
 271
 272 void print_sub_aln ( Alignment *B, int *ns, int **ls);
 273 void print_aln ( Alignment *B);
 274 FILE * output_aln( Alignment *B, FILE *fp);
 275
 276
 277 FILE * output_aln_score ( Alignment *B, FILE *fp);
 278 FILE * output_aln_with_res_number ( Alignment *B, FILE *fp);
 279
 280
 281 FILE* output_Alignment ( Alignment *B, FILE *fp);
 282 FILE* output_Alignment_without_header ( Alignment *B, FILE *fp);
 283 FILE * output_Alignment_score ( Alignment *B, FILE *fp);
 284 FILE * output_Alignment_with_res_number ( Alignment *B, FILE *fp);
 285 void output_constraints ( char *fname, char *mode, Alignment *A);
 286
 287 Alignment *input_conc_aln ( char *name, Alignment *A);
 288 void output_conc_aln ( char *name, Alignment *B);
 289 void output_glalign       ( char *name, Alignment *B, Alignment *S);
 290 void output_lalign_header( char *name, Alignment *B);
 291 void output_lalign       ( char *name, Alignment *B);
 292 void output_lalign_aln   ( char *name, Alignment *B);
 293
 294 /**************************************************************************************************/
 295 /*                                                                                                */
 296 /*                                                                                                */
 297 /*                               INPUT/OUTPUT MATRICES                                                  */
 298 /*                                                                                                */
 299 /**************************************************************************************************/
 300 int is_blast_matrix (char *fname);
 301 int is_pavie_matrix (char *fname);
 302 int is_clustalw_matrix (char *fname);
 303
 304 int is_distance_matrix_file (char *name);
 305 int is_similarity_matrix_file (char *name);
 306
 307 void aln2proba_mat (Sequence *S);
 308 void aln2mat (Sequence *S);
 309 void aln2mat_diaa (Sequence *S);
 310 int **seq2latmat ( Sequence *S, char *fname);
 311 int output_mat (int **mat, char *fname, char *alp, int offset);
 312 int ** read_blast_matrix ( char *mat_name);
 313 int output_blast_mat (int **mat, char *fname);
 314 double* mat2cmp (int **mat1, int **mat2);
 315
 316 void output_pavie_mat (int **mat, char *fname, double gep, char *alp);
 317 int ** read_pavie_matrix ( char *mat_name);
 318
 319 /****************************************************************************************************/
 320 /***************************                                    *************************************/
 321 /***************************             PROCESSING             *************************************/
 322 /***************************                                    *************************************/
 323 /*******************************************************************************************/
 324 /*                                                                                         */
 325 /*                                                                                         */
 326 /*                              THREADING                                                  */
 327 /***************************************************************************************** */
 328
 329
 330
 331
 332 Structure * declare_rna_structure_num (Sequence *SA);
 333
 334 char *thread_aa_seq_on_dna_seq( char *s);
 335 void thread_seq_struc2aln ( Alignment *A, Sequence *ST);
 336 Alignment *thread_dnaseq_on_prot_aln (Sequence *S, Alignment *A);
 337 void cache_id ( Alignment *A);
 338
 339
 340
 341 int process_est_sequence ( Sequence *S, int *cluster_list);
 342 char * invert_seq ( char *seq);
 343 int get_best_match ( char *seq1, char *seq2);
 344 int** extract_m_diag_streches ( int ** m, int l1, int l2,char *seq1, char *seq2, int *n_mdiag);
 345 int is_strech ( char *AA, char *seq1, char *seq2, int len, int x, int y);
 346
 347 int search_for_cluster ( int seq, int cluster_number, int *cluster_list, int T, int nseq, int **S);
 348 int * SHC ( int nseq, int **NST, int **ST);
 349 int mutate_sol (int *sol, int nseq);
 350 int evaluate_sol ( int*sol, int nseq, int **ST, int **NST);
 351
 352
 353
 354 char **make_symbols ( char *name, int *n);
 355 Alignment *code_dna_aln (Alignment *A);
 356 char* back_translate_dna_codon ( char aa, int deterministic);
 357 int translate_dna_codon ( char *seq, char stop);
 358 char* mutate_amino_acid ( char aa, char *mode);
 359 Alignment * mutate_aln ( Alignment *A, char *r);
 360
 361 int extend_seqaln (Sequence *S, Alignment *A);
 362 int unextend_seqaln (Sequence *S, Alignment *A);
 363 char *extend_seq (char *seq);
 364 char *unextend_seq (char *seq);
 365
 366 Sequence * transform_sequence ( Sequence *S, char *mode);
 367 Alignment *translate_splice_dna_aln (Alignment *A,Alignment *ST );
 368 Alignment * mutate_cdna_aln ( Alignment *A);
 369
 370 char *test_dna2gene (char *dna, int *w);
 371 Sequence *dnaseq2geneseq (Sequence *S, int **w);
 372
 373 int ** shift_res_weights ( Sequence *R, int **w, int shift);
 374 int res_weights2min(Sequence *R, int **w);
 375 int res_weights2max(Sequence *R, int **w);
 376 int res_weights2avg(Sequence *R, int **w);
 377 int output_wexons (char *name, Alignment *A);
 378 int scan_res_weights4ac (Sequence *R, int **w, int start, int end, int step);
 379 float *res_weights2accuracy_counts ( Sequence *R, int **w,int T, float *result);
 380 float* genepred_seq2accuracy_counts (Sequence *R, Sequence *T,float *result);
 381 void genepred_seq2accuracy_counts4all (Sequence *R, Sequence *Ts); //JM
 382 float* genepred2accuracy_counts     (char *ref,  char *target , float *result);
 383
 384 char *dna2gene (char *dna, int *w);
 385 char * translate_dna_seq_on3frame (  char *dna_seq, char stop, char *prot);
 386
 387 char * translate_dna_seq ( char *dna_seq, int frame, char stop, char *prot);
 388 int is_stop (char r1, char r2, char r3);
 389 int seq2tblastx_db (char *file,Sequence *S, int strand);
 390 int seq2blastdb (char *out, Sequence *S);
 391 char * back_translate_dna_seq ( char *in_seq,char *out_seq, int mode);
 392 Alignment *back_translate_dna_aln (Alignment *A);
 393 Sequence  *translate_dna_seqS     (Sequence *S, int frame, int stop);
 394 Alignment *translate_dna_aln (Alignment *A, int frame);
 395 char *dna_seq2pep_seq (char *seq, int frame);
 396
 397 Alignment *clean_gdna_aln (Alignment *A);
 398 Alignment *clean_cdna_aln (Alignment *A);
 399 Alignment *clean_est      (Alignment *A);
 400 /**************************************************************************************************/
 401 /********************************                      ********************************************/
 402 /********************************    PROCESSING        ********************************************/
 403 /*************** ****************                      ********************************************/
 404 void modify_data  (Sequence_data_struc *D1, Sequence_data_struc *D2, Sequence_data_struc *DST, char **action_list,int n_actions, Action_data_struc *RAD);
 405
 406 //
 407 // Name MAnipulation
 408 //
 409
 410 Alignment *clean_aln (Alignment *A);
 411 Sequence *clean_sequence ( Sequence *S);
 412 char ** translate_names (int n, char **name);
 413 char * translate_name ( char *name);
 414 char *decode_name (char *name, int mode);
 415 FILE * display_sequences_names (Sequence *S, FILE *fp, int check_pdb_status, int print_templates);
 416 Sequence *add_file2file_list (char *name, Sequence *S);
 417
 418 #endif