diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 33 |
3 files changed, 22 insertions, 21 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 51aa1622..0c1cea0e 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -498,7 +498,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap if bool(trait.description_display): results_dict['description'] = trait.description_display if bool(trait.mean): - results_dict['mean'] = float(trait.mean) + results_dict['mean'] = f"{float(trait.mean):.3f}" if trait.LRS_score_repr != "N/A": results_dict['lrs_score'] = f"{float(trait.LRS_score_repr):.1f}" results_dict['lrs_location'] = trait.LRS_location_repr diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 02f91a32..61e4897c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -31,7 +31,8 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) this_chromosomes = this_dataset.species.chromosomes.chromosomes - this_chromosomes_name=[chromosome.name for chromosome in this_chromosomes] + this_chromosomes_name=[this_chromosomes[chromosome].name for chromosome in this_chromosomes] + chr_list_string=",".join(this_chromosomes_name) if covariates != "": @@ -45,7 +46,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf genofile_name, TEMPDIR, k_output_filename) - logger.debug("k_command:" + generate_k_command) + os.system(generate_k_command) gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), @@ -77,7 +78,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf TEMPDIR, k_output_filename) - logger.debug("k_command:" + generate_k_command) os.system(generate_k_command) gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), @@ -93,8 +93,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf else: gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename) - - logger.debug("gemma_command:" + gemma_command) os.system(gemma_command) else: gwa_output_filename = output_files diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index aa74abf5..06ee9056 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -80,19 +80,21 @@ <input type="hidden" name="database_name" id="database_name" value="None"> <input type="hidden" name="export_data" id="export_data" value=""> <input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ dataset.name }}_correlation"> - <button class="btn btn-default" id="export_traits">Download CSV</button> <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search Table For ..."> <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ..."> <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button> <button id="redraw" class="btn btn-default" type="button">Reset Columns</button> </form> <br /> + <div id="export_options"></div> {% if target_dataset.type != "Publish" %} <br /> - <button id="more_options" class="btn btn-primary">More Options...</button> + <div style="float: left; clear: left; margin-top: 10px; margin-bottom: 20px;"> + <button id="more_options" class="btn btn-primary">More Options...</button> + </div> <br /> <br /> - <div id="filter_options" style="display: none;"> + <div id="filter_options" style="display: none; float: left; clear: left;"> <span style="border: 1px dashed #999999; padding: 8px; background-color: #ddf; font-size: 12px;"> <button id="select_traits" class="btn btn-primary" style="font-size: 12px; padding: 2px 3px;">Select Traits</button> with r > <input type="text" name="r_greater_select" value="-1.0" size="6" maxlength="10"> @@ -115,7 +117,7 @@ </div> {% endif %} </div> - <div class="show-hide-container"> + <div class="show-hide-container" style="float: left; clear: left;"> <b>Show/Hide Columns:</b> <br> <button class="toggle-vis" data-column="1">Index</button> @@ -174,7 +176,7 @@ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> - <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> <script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script> @@ -259,17 +261,14 @@ $(document).ready( function () { table_conf = { buttons: [ - { - extend: 'columnsToggle', - columns: function( idx, data, node ) { - if (idx != 0) { - return true; - } else { - return false; - } - }, - postfixButtons: [ 'colvisRestore' ] + { + extend: 'csvHtml5', + text: 'Download <span class="glyphicon glyphicon-download"></span>', + className: 'btn btn-default', + exportOptions: { + columns: 'th:not(:first-child)' } + } ], 'drawCallback': function( settings ) { $('#trait_table tr').off().on("click", function(event) { @@ -544,6 +543,10 @@ trait_table = $('#trait_table').DataTable(table_conf); + trait_table.buttons().container().appendTo('#export_options') + + $('.buttons-csv').removeClass('dt-button') + trait_table.on( 'order.dt search.dt draw.dt', function () { trait_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) { cell.innerHTML = i+1; |