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C: build_ref_db: added progress display for each step

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This commit is contained in:
Celine Mercier
2020-04-18 14:24:08 +02:00
parent 0f745e0113
commit 67bdee105a
1 changed files with 24 additions and 5 deletions
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29
src/build_reference_db.c
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@ -157,7 +157,7 @@ int build_reference_db(const char* dms_name,
ecotx_t* lca_2 = NULL; ecotx_t* lca_2 = NULL;
ecotx_t* lca = NULL; ecotx_t* lca = NULL;
index_t idx1, idx2; index_t idx1, idx2;
index_t i, j, k; index_t i, j, k, count;
int32_t taxid_array_length; int32_t taxid_array_length;
int32_t score_array_length; int32_t score_array_length;
int32_t taxid_array_writable_length; int32_t taxid_array_writable_length;
@ -185,6 +185,7 @@ int build_reference_db(const char* dms_name,
matrix_view_name = strcpy(matrix_view_name, o_view_name); matrix_view_name = strcpy(matrix_view_name, o_view_name);
strcat(matrix_view_name, "_matrix"); strcat(matrix_view_name, "_matrix");
fprintf(stderr, "Aligning queries with reference database...\n");
if (obi_lcs_align_one_column(dms_name, if (obi_lcs_align_one_column(dms_name,
refs_view_name, refs_view_name,
"", "",
@ -320,13 +321,19 @@ int build_reference_db(const char* dms_name,
return -1; return -1;
} }
count = (matrix_with_lca_view->infos)->line_count;
fprintf(stderr, "Computing LCAs...\n");
// Compute all the LCAs // Compute all the LCAs
// For each pair // For each pair
for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++) for (i=0; i<count; i++)
{ {
if (! keep_running) if (! keep_running)
return -1; return -1;
if (i%1000 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) count)*100);
// Read all taxids associated with the first sequence and compute their LCA // Read all taxids associated with the first sequence and compute their LCA
// Read line index // Read line index
idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0); idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
@ -363,6 +370,7 @@ int build_reference_db(const char* dms_name,
return -1; return -1;
} }
} }
fprintf(stderr,"\rDone : 100 %% \n");
// Clone refs view, add 2 arrays columns for lca and score, compute and write them // Clone refs view, add 2 arrays columns for lca and score, compute and write them
@ -442,13 +450,18 @@ int build_reference_db(const char* dms_name,
return -1; return -1;
} }
fprintf(stderr, "Building LCA arrays...\n");
// For each sequence, look for all its alignments in the matrix, and for each different LCA taxid/score, order them and write them // For each sequence, look for all its alignments in the matrix, and for each different LCA taxid/score, order them and write them
// Going through matrix once, filling refs arrays on the go for efficiency // Going through matrix once, filling refs arrays on the go for efficiency
for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++) for (i=0; i<count; i++)
{ {
if (! keep_running) if (! keep_running)
return -1; return -1;
if (i%1000 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) count)*100);
// Read ref line indexes // Read ref line indexes
idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0); idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
idx2 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx2_column, i, 0); idx2 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx2_column, i, 0);
@ -769,11 +782,17 @@ int build_reference_db(const char* dms_name,
} }
} }
} }
fprintf(stderr,"\rDone : 100 %% \n");
fprintf(stderr, "Writing results...\n");
count = (o_view->infos)->line_count;
// Fill empty LCA informations (because filling from potentially sparse alignment matrix) with the sequence taxid // Fill empty LCA informations (because filling from potentially sparse alignment matrix) with the sequence taxid
score=1.0; // technically getting LCA of identical sequences score=1.0; // technically getting LCA of identical sequences
for (i=0; i<(o_view->infos)->line_count; i++) for (i=0; i<count; i++)
{ {
if (i%1000 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) count)*100);
obi_get_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, i, &taxid_array_length); obi_get_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, i, &taxid_array_length);
if (taxid_array_length == 0) // no LCA set if (taxid_array_length == 0) // no LCA set
{ {
@ -799,6 +818,7 @@ int build_reference_db(const char* dms_name,
} }
} }
} }
fprintf(stderr,"\rDone : 100 %% \n");
// Add information about the threshold used to build the DB // Add information about the threshold used to build the DB
snprintf(threshold_str, 5, "%f", threshold); snprintf(threshold_str, 5, "%f", threshold);
@ -858,7 +878,6 @@ int build_reference_db(const char* dms_name,
free(matrix_view_name); free(matrix_view_name);
free(matrix_with_lca_view_name); free(matrix_with_lca_view_name);
fprintf(stderr,"\rDone : 100 %% \n");
return 0; return 0;
} }