/**************************************************************************** * LCS sequence alignment functions * ****************************************************************************/ /** * @file obi_lcs.c * @author Celine Mercier (celine.mercier@metabarcoding.org) * @date May 4th 2016 * @brief Functions handling LCS sequence alignments. */ //#define OMP_SUPPORT // TODO #ifdef OMP_SUPPORT #include #endif #include #include #include #include "obi_lcs.h" #include "obidebug.h" #include "obierrno.h" #include "obisig.h" #include "obitypes.h" #include "obiview.h" #include "sse_banded_LCS_alignment.h" #include "upperband.h" #include "obiblob.h" #define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?) /************************************************************************** * * D E C L A R A T I O N O F T H E P R I V A T E F U N C T I O N S * **************************************************************************/ /** * @brief Internal function creating the columns where the alignment results are written. * * @param output_view A pointer on the writable view where the columns should be created. * @param id1_indexer_name The name of the indexer where the id of the 1st sequence aligned is indexed. * @param id2_indexer_name The name of the indexer where the id of the 2nd sequence aligned is indexed. * @param seq1_indexer_name The name of the indexer where the 1st sequence aligned is indexed (needed only if print_seq is True). * @param seq2_indexer_name The name of the indexer where the 2nd sequence aligned is indexed (needed only if print_seq is True). * @param print_seq A boolean indicating whether the aligned sequences should be copied in the output view. * @param print_count A boolean indicating whether the aligned sequence counts should be copied in the output view. * @param normalize Whether the score should be normalized with the reference sequence length. * @param reference The reference length. 0: The alignement length; 1: The longest sequence's length; 2: The shortest sequence's length. * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false). * * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since December 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ static int create_alignment_output_columns(Obiview_p output_view, const char* id1_indexer_name, const char* id2_indexer_name, const char* seq1_indexer_name, const char* seq2_indexer_name, bool print_seq, bool print_count, bool normalize, int reference, bool similarity_mode); /** * @brief Internal function printing the result of one alignment to the output view. * * @param output_view A pointer on the writable view where the result should be written. * @param line The line in the output view where the result should be written. * @param idx1_column A pointer on the column where the index referring to the line of the first sequence aligned in the input view should be written. * @param idx2_column A pointer on the column where the index referring to the line of the second sequence aligned in the input view should be written. * @param idx1 The index referring to the line of the first sequence aligned in the input view. * @param idx2 The index referring to the line of the second sequence aligned in the input view. * @param id1_column A pointer on the column where the identifier of the first sequence aligned should be written. * @param id2_column A pointer on the column where the identifier of the second sequence aligned should be written. * @param id1_idx The index of the identifier of the first sequence aligned. * @param id2_idx The index of the identifier of the second sequence aligned. * @param print_seq A boolean indicating whether the aligned sequences should be copied in the output view. * @param seq1_column A pointer on the column where the first sequence aligned should be written. * @param seq2_column A pointer on the column where the second sequence aligned should be written. * @param seq1_idx The index of the sequence of the first sequence aligned. * @param seq2_idx The index of the sequence of the second sequence aligned. * @param print_count A boolean indicating whether the aligned sequence counts should be copied in the output view. * @param count1_column A pointer on the column where the count of the first sequence aligned should be written. * @param count2_column A pointer on the column where the count of the second sequence aligned should be written. * @param count1 The count of the first sequence aligned. * @param count2 The count of the second sequence aligned. * @param ali_length_column A pointer on the column where the alignment length should be written. * @param ali_length The alignment length. * @param lcs_length_column A pointer on the column where the LCS length should be written. * @param lcs_length The LCS length. * @param score_column A pointer on the column where the score should be written. * @param score The alignment score. * @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length. * @param normalize Whether the score should be normalized with the reference sequence length. * @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false). * * @retval 0 if the operation was successfully completed. * @retval -1 if an error occurred. * * @since December 2016 * @author Celine Mercier (celine.mercier@metabarcoding.org) */ static int print_alignment_result(Obiview_p output_view, index_t line, OBIDMS_column_p idx1_column, OBIDMS_column_p idx2_column, index_t idx1, index_t idx2, OBIDMS_column_p id1_column, OBIDMS_column_p id2_column, index_t id1_idx, index_t id2_idx, bool print_seq, OBIDMS_column_p seq1_column, OBIDMS_column_p seq2_column, index_t seq1_idx, index_t seq2_idx, bool print_count, OBIDMS_column_p count1_column, OBIDMS_column_p count2_column, int count1, int count2, OBIDMS_column_p ali_length_column, int ali_length, OBIDMS_column_p lcs_length_column, int lcs_length, OBIDMS_column_p score_column, double score, int reference, bool normalize, bool similarity_mode); /************************************************************************ * * D E F I N I T I O N O F T H E P R I V A T E F U N C T I O N S * ************************************************************************/ static int create_alignment_output_columns(Obiview_p output_view, const char* id1_indexer_name, const char* id2_indexer_name, const char* seq1_indexer_name, const char* seq2_indexer_name, bool print_seq, bool print_count, bool normalize, int reference, bool similarity_mode) { // Create the column for the ids of the 1st sequence aligned if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the first column for the sequence ids when aligning"); return -1; } // Create the column for the ids of the 2nd sequence aligned if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, false, false, false, false, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the second column for the sequence ids when aligning"); return -1; } // Create the column for the index (in the input view) of the first sequences aligned if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the first column for the sequence indices when aligning"); return -1; } // Create the column for the index (in the input view) of the second sequences aligned if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the second column for the sequence indices when aligning"); return -1; } // Create the column for the LCS length if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the column for the LCS length when aligning"); return -1; } // Create the column for the alignment length if it is computed if ((reference == ALILEN) && (normalize || !similarity_mode)) { if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the column for the alignment length when aligning"); return -1; } } // Create the column for the alignment score if (normalize) { if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0) { obidebug(1, "\nError creating the column for the score when aligning"); return -1; } } else { if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0) { obidebug(1, "\nError creating the column for the score when aligning"); return -1; } } if (print_seq) { // Create the column for the first sequences aligned if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the first column for the sequences when aligning"); return -1; } // Create the column for the second sequences aligned if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, false, false, false, false, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the second column for the sequences when aligning"); return -1; } } if (print_count) { // Create the column for the count of the first sequences aligned if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the first column for the sequence counts when aligning"); return -1; } // Create the column for the count of the second sequences aligned if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, false, false, false, false, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0) { obidebug(1, "\nError creating the second column for the sequence counts when aligning"); return -1; } } return 0; } static int print_alignment_result(Obiview_p output_view, index_t line, OBIDMS_column_p idx1_column, OBIDMS_column_p idx2_column, index_t idx1, index_t idx2, OBIDMS_column_p id1_column, OBIDMS_column_p id2_column, index_t id1_idx, index_t id2_idx, bool print_seq, OBIDMS_column_p seq1_column, OBIDMS_column_p seq2_column, index_t seq1_idx, index_t seq2_idx, bool print_count, OBIDMS_column_p count1_column, OBIDMS_column_p count2_column, int count1, int count2, OBIDMS_column_p ali_length_column, int ali_length, OBIDMS_column_p lcs_length_column, int lcs_length, OBIDMS_column_p score_column, double score, int reference, bool normalize, bool similarity_mode) { // Write line indices of the input view in the output view (to easily refer to the input sequences from the output view) if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, idx1_column, line, 0, idx1) < 0) { obidebug(1, "\nError writing idx1 in a column"); return -1; } if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, idx2_column, line, 0, idx2) < 0) { obidebug(1, "\nError writing idx2 in a column"); return -1; } // Write ids in output view if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, id1_column, line, 0, id1_idx) < 0) { obidebug(1, "\nError writing id1 in a column"); return -1; } if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, id2_column, line, 0, id2_idx) < 0) { obidebug(1, "\nError writing id2 in a column"); return -1; } // Write the sequences if needed if (print_seq) { if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, seq1_column, line, 0, seq1_idx) < 0) { obidebug(1, "\nError writing seq1 in a column"); return -1; } if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, seq2_column, line, 0, seq2_idx) < 0) { obidebug(1, "\nError writing seq2 in a column"); return -1; } } // Write the counts if needed if (print_count) { if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, count1_column, line, 0, count1) < 0) { obidebug(1, "\nError writing count1 in a column"); return -1; } if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, count2_column, line, 0, count2) < 0) { obidebug(1, "\nError writing count2 in a column"); return -1; } } // Write the alignment length if it was computed if ((reference == ALILEN) && (normalize || !similarity_mode)) { if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, ali_length_column, line, 0, ali_length) < 0) { obidebug(1, "\nError writing alignment length in a column"); return -1; } } // Write the LCS length if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, lcs_length_column, line, 0, lcs_length) < 0) { obidebug(1, "\nError writing LCS length in a column"); return -1; } // Write score if (normalize) { if (obi_set_float_with_elt_idx_and_col_p_in_view(output_view, score_column, line, 0, (obifloat_t) score) < 0) { obidebug(1, "\nError writing alignment score in a column"); return -1; } } else { if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, score_column, line, 0, (obiint_t) score) < 0) { obidebug(1, "\nError writing alignment score in a column"); return -1; } } return 0; } /********************************************************************** * * D E F I N I T I O N O F T H E P U B L I C F U N C T I O N S * **********************************************************************/ int obi_lcs_align_one_column(const char* dms_name, const char* seq_view_name, const char* seq_column_name, const char* seq_elt_name, const char* id_column_name, const char* output_view_name, const char* output_view_comments, bool print_seq, bool print_count, double threshold, bool normalize, int reference, bool similarity_mode, int thread_count) { index_t i, j, k; index_t seq_count; index_t id1_idx, id2_idx; index_t seq1_idx, seq2_idx; int count1 = 0; int count2 = 0; double score; int lcs_length; int ali_length; Kmer_table_p ktable; Obi_blob_p blob1; Obi_blob_p blob2; int lcs_min; index_t seq_elt_idx; OBIDMS_p dms = NULL; Obiview_p seq_view = NULL; Obiview_p output_view = NULL; OBIDMS_column_p iseq_column = NULL; OBIDMS_column_p i_count_column = NULL; OBIDMS_column_p id_column = NULL; OBIDMS_column_p id1_column = NULL; OBIDMS_column_p id2_column = NULL; OBIDMS_column_p seq1_column = NULL; OBIDMS_column_p seq2_column = NULL; OBIDMS_column_p count1_column = NULL; OBIDMS_column_p count2_column = NULL; OBIDMS_column_p idx1_column = NULL; OBIDMS_column_p idx2_column = NULL; OBIDMS_column_p lcs_length_column = NULL; OBIDMS_column_p ali_length_column = NULL; OBIDMS_column_p score_column = NULL; signal(SIGINT, sig_handler); k = 0; // Open DMS dms = obi_open_dms(dms_name, false); if (dms == NULL) { obidebug(1, "\nError opening the DMS"); return -1; } // Open input view seq_view = obi_open_view(dms, seq_view_name); if (seq_view == NULL) { obidebug(1, "\nError opening the input view to align"); return -1; } // Open the sequence column to align // If a column name wasn't given, open default sequence column if (strcmp(seq_column_name, "") == 0) // TODO check for NULL { if (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0) iseq_column = obi_view_get_column(seq_view, NUC_SEQUENCE_COLUMN); else { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: no column given to align"); return -1; } } else iseq_column = obi_view_get_column(seq_view, seq_column_name); if (iseq_column == NULL) { obidebug(1, "\nError getting the column to align"); return -1; } // Check column type if ((iseq_column->header)->returned_data_type != OBI_SEQ) { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: column given to align is not an OBI_SEQ column"); return -1; } // Get element index of the sequence to align in each line to compute it only once if ((strcmp(seq_elt_name, "") != 0) && (seq_elt_name != NULL)) { seq_elt_idx = obi_column_get_element_index_from_name(iseq_column, seq_elt_name); if (seq_elt_idx == OBIIdx_NA) { obidebug(1, "\nError getting the sequence index in a column line when aligning"); return -1; } } else seq_elt_idx = 0; // Open the ID column, containing the identifiers of the sequences to align // If a column name wasn't given, open default ID column if (strcmp(id_column_name, "") == 0) { if (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0) id_column = obi_view_get_column(seq_view, ID_COLUMN); else { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: no ID column given"); return -1; } } else id_column = obi_view_get_column(seq_view, id_column_name); if (id_column == NULL) { obidebug(1, "\nError getting the ID column"); return -1; } // Open the input count column if (print_count) { i_count_column = obi_view_get_column(seq_view, COUNT_COLUMN); if (i_count_column == NULL) { obidebug(1, "\nError getting the input COUNT column"); return -1; } } // Create the output view output_view = obi_new_view(dms, output_view_name, NULL, NULL, output_view_comments); if (output_view == NULL) { obidebug(1, "\nError creating the output view when aligning"); return -1; } // Create the output columns if (create_alignment_output_columns(output_view, (id_column->header)->indexer_name, (id_column->header)->indexer_name, (iseq_column->header)->indexer_name, (iseq_column->header)->indexer_name, print_seq, print_count, normalize, reference, similarity_mode) < 0) return -1; id1_column = obi_view_get_column(output_view, ID1_COLUMN_NAME); id2_column = obi_view_get_column(output_view, ID2_COLUMN_NAME); idx1_column = obi_view_get_column(output_view, IDX1_COLUMN_NAME); idx2_column = obi_view_get_column(output_view, IDX2_COLUMN_NAME); lcs_length_column = obi_view_get_column(output_view, LCS_LENGTH_COLUMN_NAME); if ((reference == ALILEN) && (normalize || !similarity_mode)) ali_length_column = obi_view_get_column(output_view, ALI_LENGTH_COLUMN_NAME); score_column = obi_view_get_column(output_view, SCORE_COLUMN_NAME); if (print_seq) { seq1_column = obi_view_get_column(output_view, SEQ1_COLUMN_NAME); seq2_column = obi_view_get_column(output_view, SEQ2_COLUMN_NAME); } if (print_count) { count1_column = obi_view_get_column(output_view, COUNT1_COLUMN_NAME); count2_column = obi_view_get_column(output_view, COUNT2_COLUMN_NAME); } // Build kmer tables ktable = hash_seq_column(seq_view, iseq_column, seq_elt_idx); if (ktable == NULL) { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError building kmer tables before aligning"); return -1; } seq_count = (seq_view->infos)->line_count; #ifdef OMP_SUPPORT omp_set_num_threads(thread_count); #pragma omp parallel for #endif for (i=0; i < (seq_count - 1); i++) { if (i%100 == 0) fprintf(stderr,"\rDone : %f %% ", (i / (float) seq_count)*100); if (! keep_running) return -1; // Get first id idx id1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, id_column, i, 0); // TODO Could there be multiple IDs per line? // Get first sequence and its index seq1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, i, seq_elt_idx); blob1 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, i, seq_elt_idx); if (blob1 == NULL) { obidebug(1, "\nError retrieving sequences to align"); return -1; } for (j=i+1; j < seq_count; j++) { // Get second sequence and its index seq2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, j, seq_elt_idx); blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, j, seq_elt_idx); if (blob2 == NULL) { obidebug(1, "\nError retrieving sequences to align"); return -1; } // Check if the sequences are identical in a quick way (same index in the same indexer) if (obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, i, seq_elt_idx) == obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, j, seq_elt_idx)) { if (similarity_mode && normalize) score = 1.0; else if (!similarity_mode) score = 0.0; else score = blob1->length_decoded_value; } else // the sequences aren't identical { // kmer filter align_filters(ktable, blob1, blob2, i, j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, false); // Compute alignment score if ((threshold == 0) || (score == -1.0)) // no threshold, or filter passed: align score = obiblob_sse_banded_lcs_align(blob1, blob2, threshold, normalize, reference, similarity_mode, &lcs_length, &ali_length); } if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold)))) { // Print result // Get second id idx id2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, id_column, j, 0); // Get counts // TODO use array for efficiency? if (print_count) { count1 = obi_get_int_with_elt_idx_and_col_p_in_view(seq_view, i_count_column, i, 0); count2 = obi_get_int_with_elt_idx_and_col_p_in_view(seq_view, i_count_column, j, 0); } if (print_alignment_result(output_view, k, idx1_column, idx2_column, i, j, id1_column, id2_column, id1_idx, id2_idx, print_seq, seq1_column, seq2_column, seq1_idx, seq2_idx, print_count, count1_column, count2_column, count1, count2, ali_length_column, ali_length, lcs_length_column, lcs_length, score_column, score, reference, normalize, similarity_mode) < 0) return -1; k++; } } } fprintf(stderr,"\rDone : 100 %% \n"); // Close views if (obi_save_and_close_view(seq_view) < 0) { obidebug(1, "\nError closing the input view after aligning"); return -1; } if (obi_save_and_close_view(output_view) < 0) { obidebug(1, "\nError closing the output view after aligning"); return -1; } if (obi_close_dms(dms, false) < 0) { obidebug(1, "\nError closing the DMS after aligning"); return -1; } free_kmer_tables(ktable, seq_count); return 0; } int obi_lcs_align_two_columns(const char* dms_name, const char* seq1_view_name, const char* seq2_view_name, const char* seq1_column_name, const char* seq2_column_name, const char* seq1_elt_name, const char* seq2_elt_name, const char* id1_column_name, const char* id2_column_name, const char* output_view_name, const char* output_view_comments, bool print_seq, bool print_count, double threshold, bool normalize, int reference, bool similarity_mode) { index_t i, j, k; index_t seq1_count; index_t seq2_count; index_t id1_idx, id2_idx; index_t seq1_idx, seq2_idx; int count1 = 0; int count2 = 0; double score; int lcs_length; int ali_length; Kmer_table_p ktable; Obi_blob_p blob1; Obi_blob_p blob2; int lcs_min; index_t seq1_elt_idx; index_t seq2_elt_idx; bool same_indexer; OBIDMS_p dms = NULL; Obiview_p seq1_view = NULL; Obiview_p seq2_view = NULL; Obiview_p output_view = NULL; OBIDMS_column_p i_seq1_column = NULL; OBIDMS_column_p i_seq2_column = NULL; OBIDMS_column_p i_id1_column = NULL; OBIDMS_column_p i_id2_column = NULL; OBIDMS_column_p i_count1_column = NULL; OBIDMS_column_p i_count2_column = NULL; OBIDMS_column_p id1_column = NULL; OBIDMS_column_p id2_column = NULL; OBIDMS_column_p seq1_column = NULL; OBIDMS_column_p seq2_column = NULL; OBIDMS_column_p count1_column = NULL; OBIDMS_column_p count2_column = NULL; OBIDMS_column_p idx1_column = NULL; OBIDMS_column_p idx2_column = NULL; OBIDMS_column_p lcs_length_column = NULL; OBIDMS_column_p ali_length_column = NULL; OBIDMS_column_p score_column = NULL; signal(SIGINT, sig_handler); k = 0; // Open DMS dms = obi_open_dms(dms_name, false); if (dms == NULL) { obidebug(1, "\nError opening the DMS to align"); return -1; } // Open the first input view seq1_view = obi_open_view(dms, seq1_view_name); if (seq1_view == NULL) { obidebug(1, "\nError opening the first input view to align"); return -1; } // Open the second input view. Same as 1st if "" if (strcmp(seq2_view_name, "") == 0) seq2_view = seq1_view; else { seq2_view = obi_open_view(dms, seq2_view_name); if (seq2_view == NULL) { obidebug(1, "\nError opening the second input view to align"); return -1; } } // Open the first sequence column to align // If a column name wasn't given, open default sequence column if (strcmp(seq1_column_name, "") == 0) { if (strcmp((seq1_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0) i_seq1_column = obi_view_get_column(seq1_view, NUC_SEQUENCE_COLUMN); else { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: no first column given to align"); return -1; } } else i_seq1_column = obi_view_get_column(seq1_view, seq1_column_name); if (i_seq1_column == NULL) { obidebug(1, "\nError getting the first column to align"); return -1; } // Check column type if ((i_seq1_column->header)->returned_data_type != OBI_SEQ) { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: first column given to align is not an OBI_SEQ column"); return -1; } // Open the second sequence column to align // If a column name wasn't given, open default sequence column if (strcmp(seq2_column_name, "") == 0) { if (strcmp((seq2_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0) i_seq2_column = obi_view_get_column(seq2_view, NUC_SEQUENCE_COLUMN); else { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: no second column given to align"); return -1; } } else i_seq2_column = obi_view_get_column(seq2_view, seq2_column_name); if (i_seq2_column == NULL) { obidebug(1, "\nError getting the second column to align"); return -1; } // Check that the sequence columns are not both the default NUC_SEQ column of the same view if (i_seq1_column == i_seq2_column) { obidebug(1, "\nError: trying to align a column with itself (default NUC_SEQ column of the same view)"); return -1; } // Check column type if ((i_seq2_column->header)->returned_data_type != OBI_SEQ) { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: second column given to align is not an OBI_SEQ column"); return -1; } // Get element index of the sequence to align in each line of the first column to compute it only once if ((strcmp(seq1_elt_name, "") != 0) && (seq1_elt_name != NULL)) { seq1_elt_idx = obi_column_get_element_index_from_name(i_seq1_column, seq1_elt_name); if (seq1_elt_idx == OBIIdx_NA) { obidebug(1, "\nError getting the sequence index in a column line when aligning"); return -1; } } else seq1_elt_idx = 0; // Get element index of the sequence to align in each line of the second column to compute it only once if ((strcmp(seq2_elt_name, "") != 0) && (seq2_elt_name != NULL)) { seq2_elt_idx = obi_column_get_element_index_from_name(i_seq2_column, seq2_elt_name); if (seq2_elt_idx == OBIIdx_NA) { obidebug(1, "\nError getting the sequence index in a column line when aligning"); return -1; } } else seq2_elt_idx = 0; // Open the first ID column, containing the identifiers of the first sequence to align // If a column name wasn't given, open default ID column if (strcmp(id1_column_name, "") == 0) { if (strcmp((seq1_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0) i_id1_column = obi_view_get_column(seq1_view, ID_COLUMN); else { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: no first ID column given"); return -1; } } else i_id1_column = obi_view_get_column(seq1_view, id1_column_name); if (i_id1_column == NULL) { obidebug(1, "\nError getting the first ID column"); return -1; } // Open the second ID column, containing the identifiers of the second sequence to align // If a column name wasn't given, open default ID column if (strcmp(id2_column_name, "") == 0) { if (strcmp((seq2_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0) i_id2_column = obi_view_get_column(seq2_view, ID_COLUMN); else { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError: no second ID column given"); return -1; } } else i_id2_column = obi_view_get_column(seq2_view, id2_column_name); if (i_id2_column == NULL) { obidebug(1, "\nError getting the second ID column"); return -1; } // Open the input count columns if (print_count) { i_count1_column = obi_view_get_column(seq1_view, COUNT_COLUMN); if (i_count1_column == NULL) { obidebug(1, "\nError getting the first input COUNT column"); return -1; } i_count2_column = obi_view_get_column(seq2_view, COUNT_COLUMN); if (i_count2_column == NULL) { obidebug(1, "\nError getting the second input COUNT column"); return -1; } } // Create the output view output_view = obi_new_view(dms, output_view_name, NULL, NULL, output_view_comments); if (output_view == NULL) { obidebug(1, "\nError creating the output view when aligning"); return -1; } // Create the output columns if (create_alignment_output_columns(output_view, (i_id1_column->header)->indexer_name, (i_id2_column->header)->indexer_name, (i_seq1_column->header)->indexer_name, (i_seq2_column->header)->indexer_name, print_seq, print_count, normalize, reference, similarity_mode) < 0) return -1; id1_column = obi_view_get_column(output_view, ID1_COLUMN_NAME); id2_column = obi_view_get_column(output_view, ID2_COLUMN_NAME); idx1_column = obi_view_get_column(output_view, IDX1_COLUMN_NAME); idx2_column = obi_view_get_column(output_view, IDX2_COLUMN_NAME); lcs_length_column = obi_view_get_column(output_view, LCS_LENGTH_COLUMN_NAME); if ((reference == ALILEN) && (normalize || !similarity_mode)) ali_length_column = obi_view_get_column(output_view, ALI_LENGTH_COLUMN_NAME); score_column = obi_view_get_column(output_view, SCORE_COLUMN_NAME); if (print_seq) { seq1_column = obi_view_get_column(output_view, SEQ1_COLUMN_NAME); seq2_column = obi_view_get_column(output_view, SEQ2_COLUMN_NAME); } if (print_count) { count1_column = obi_view_get_column(output_view, COUNT1_COLUMN_NAME); count2_column = obi_view_get_column(output_view, COUNT2_COLUMN_NAME); } // Check if the sequence columns share the same indexer (allows for quick checking of sequence equality) if (strcmp((i_seq1_column->header)->indexer_name, (i_seq2_column->header)->indexer_name) == 0) same_indexer = true; else same_indexer = false; // Build kmer tables ktable = hash_two_seq_columns(seq1_view, i_seq1_column, seq1_elt_idx, seq2_view, i_seq2_column, seq2_elt_idx); if (ktable == NULL) { obi_set_errno(OBI_ALIGN_ERROR); obidebug(1, "\nError building kmer tables before aligning"); return -1; } // TODO check this if (!similarity_mode && normalize && (threshold > 0)) threshold = 1.0 - threshold; seq1_count = (seq1_view->infos)->line_count; seq2_count = (seq2_view->infos)->line_count; for (i=0; i < seq1_count; i++) { if (i%100 == 0) fprintf(stderr,"\rDone : %f %% ", (i / (float) seq1_count)*100); // Get id index of first sequence id1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq1_view, i_id1_column, i, 0); // TODO Could there be multiple IDs per line? // Get first sequence and its index seq1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq1_view, i_seq1_column, i, seq1_elt_idx); blob1 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq1_view, i_seq1_column, i, seq1_elt_idx); if (blob1 == NULL) { obidebug(1, "\nError retrieving sequences to align"); return -1; } for (j=0; j < seq2_count; j++) { if (! keep_running) return -1; // Get second sequence and its index seq2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx); blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx); if (blob2 == NULL) { obidebug(1, "\nError retrieving sequences to align"); return -1; } // Check if the sequences are identical in a quick way (same index in the same indexer) if (same_indexer && (seq1_idx == seq2_idx)) { if (similarity_mode && normalize) score = 1.0; else if (!similarity_mode) score = 0.0; else score = blob1->length_decoded_value; } else // the sequences aren't identical or we don't know { // kmer filter (offset for the index of the kmer table of the 2nd sequence because the kmer tables of the 2 sequence columns are concatenated in one) align_filters(ktable, blob1, blob2, i, seq1_count+j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, !same_indexer); // Compute alignment score if ((score < 0) && ((threshold == 0) || (score == -1.0))) // (sequences are not identical), and (no threshold, or filter passed): align score = obiblob_sse_banded_lcs_align(blob1, blob2, threshold, normalize, reference, similarity_mode, &lcs_length, &ali_length); // TODO check this // if (print && !lcsmode && normalize) // score = 1.0 - score; } if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold)))) { // Print result // Get second id idx id2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq2_view, i_id2_column, j, 0); // Get counts // TODO use array for efficiency? if (print_count) { count1 = obi_get_int_with_elt_idx_and_col_p_in_view(seq1_view, i_count1_column, i, 0); count2 = obi_get_int_with_elt_idx_and_col_p_in_view(seq2_view, i_count2_column, j, 0); } if (print_alignment_result(output_view, k, idx1_column, idx2_column, i, j, id1_column, id2_column, id1_idx, id2_idx, print_seq, seq1_column, seq2_column, seq1_idx, seq2_idx, print_count, count1_column, count2_column, count1, count2, ali_length_column, ali_length, lcs_length_column, lcs_length, score_column, score, reference, normalize, similarity_mode) < 0) return -1; k++; } } } // Close views if (seq2_view != seq1_view) { if (obi_save_and_close_view(seq2_view) < 0) { obidebug(1, "\nError closing the second input view after aligning"); return -1; } } if (obi_save_and_close_view(seq1_view) < 0) { obidebug(1, "\nError closing the first input view after aligning"); return -1; } if (obi_save_and_close_view(output_view) < 0) { obidebug(1, "\nError closing the output view after aligning"); return -1; } if (obi_close_dms(dms, false) < 0) { obidebug(1, "\nError closing the DMS after aligning"); return -1; } free_kmer_tables(ktable, seq1_count + seq2_count); return 0; }