diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/plink_mapping.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/search_results.js | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/submit_bnw.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_details.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_statistics.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 6 |
9 files changed, 44 insertions, 13 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index ff1fb492..93bd9d42 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -1801,9 +1801,9 @@ class MarkerRegression(object): distScale = 10 else: distScale = 5 - for i, tickdists in enumerate(range(distScale, int(ceil(distLen)), distScale)): + for j, tickdists in enumerate(range(distScale, int(ceil(distLen)), distScale)): canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom) - if i % 2 == 0: + if j % 2 == 0: canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270) startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 3d31da1a..4de88f00 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -14,7 +14,7 @@ def run_plink(this_trait, dataset, species, vals, maf): gen_pheno_txt_file(dataset, vals) #gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename) - plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-fid --no-parents --no-sex --maf %s --missing-phenotype -9 --out %s/%s --assoc ' % ( + plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-pheno --no-fid --no-parents --no-sex --maf %s --out %s%s --assoc ' % ( flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename) logger.debug("plink_command:", plink_command) @@ -48,7 +48,7 @@ def gen_pheno_txt_file(this_dataset, vals): this_val = -9 else: this_val = vals[i] - outfile.write(line[1] + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") + outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): ped_sample_list = get_samples_from_ped_file(dataset) @@ -106,7 +106,7 @@ def parse_plink_output(output_filename, species): threshold_p_value = 1 - result_fp = open("%s/%s.qassoc"% (TMPDIR, output_filename), "rb") + result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb") header_line = result_fp.readline()# read header line line = result_fp.readline() diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index eabddbc4..8de85a86 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1918,12 +1918,12 @@ [ "797", "EPFL_AdiPro0416", - "EPFL/ETHZ BXD Brown Adipose, Total Tissue Proteome, Chow Diet (Apr16) Light SWATH **" + "EPFL/ETHZ BXD Brown Adipose, Total Tissue Proteome, Chow Diet (Apr16) Light SWATH" ], [ "798", "EPFL_AdiMitPro0416", - "EPFL/ETHZ BXD Brown Adipose, Isolated Mitochondria Proteome, Chow Diet (Apr16) Light SWATH **" + "EPFL/ETHZ BXD Brown Adipose, Isolated Mitochondria Proteome, Chow Diet (Apr16) Light SWATH" ] ], "Adipose mRNA": [ @@ -3583,7 +3583,7 @@ [ "799", "FGUCAS_BAdip0516", - "FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2 **" + "FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2" ] ], "Adrenal Gland mRNA": [ diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js index 40fdff70..2b878087 100644 --- a/wqflask/wqflask/static/new/javascript/search_results.js +++ b/wqflask/wqflask/static/new/javascript/search_results.js @@ -154,11 +154,15 @@ $(function() { } }; + submit_bnw = function() { + trait_data = get_traits_from_table("trait_table", "submit_bnw") + } + export_traits = function() { - trait_data = get_traits_from_table("trait_table") + trait_data = get_traits_from_table("trait_table", "export_csv") }; - get_traits_from_table = function(table_name) { + get_traits_from_table = function(table_name, destination) { trait_table = $('#'+table_name); table_dict = {}; @@ -199,7 +203,11 @@ $(function() { json_table_dict = JSON.stringify(table_dict); $('input[name=export_data]').val(json_table_dict); - $('#export_form').attr('action', '/export_traits_csv'); + if (destination == "export_csv"){ + $('#export_form').attr('action', '/export_traits_csv'); + } else{ + $('#export_form').attr('action', '/submit_bnw'); + } $('#export_form').submit(); }; @@ -208,6 +216,7 @@ $(function() { $("#invert").click(invert); $("#add").click(add); $("#remove").click(remove); + $("#submit_bnw").click(submit_bnw); $("#export_traits").click(export_traits); $('.trait_checkbox, .btn').click(change_buttons); });
\ No newline at end of file diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py new file mode 100644 index 00000000..59e60dfd --- /dev/null +++ b/wqflask/wqflask/submit_bnw.py @@ -0,0 +1,11 @@ +from __future__ import absolute_import, print_function, division + +from base.trait import GeneralTrait +from base import data_set +from utility import helper_functions + +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def get_bnw_input(start_vars): + logger.debug("BNW VARS:", start_vars)
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index d41f4dfb..a291baf3 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -141,7 +141,8 @@ <script type="text/javascript" src="/static/new/javascript/box_plot.js"></script> <script type="text/javascript" src="/static/new/javascript/scatterplot.js"></script> <script type="text/javascript" src="/static/new/javascript/scatter-matrix.js"></script> - <script type="text/javascript" src="/static/new/javascript/draw_probability_plot.js"></script> + <script type="text/javascript" src="/static/new/javascript/draw_probability_plot.js"></script> + <!--<script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script>--> <script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script> diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index a0c40c7f..2a62733e 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -70,6 +70,10 @@ Genotation </a> + <a href="https://www.gtexportal.org/home/gene/{{ this_trait.symbol }}" title="GTEx Portal"> + GTEx Portal + </a> + {% endif %} </td> </tr> diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 48ac468a..aa95b083 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -105,7 +105,6 @@ <option value="{{ group }}">{{ pretty_group }}</option> {% endfor %} </select> - <!--<button type="button" class="btn btn-default" id="down_prob_plot">Export as PNG</button>--> <br> <br> {% endif %} @@ -113,6 +112,7 @@ <div id="prob_plot_container"> <div id="prob_plot_title"></div> <svg></svg> + <!--<div id="prob_plot_div"></div>--> </div> <div id="shapiro_wilk_text"></div> <div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 40806450..68e779a1 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -38,6 +38,7 @@ from wqflask import gsearch from wqflask import update_search_results from wqflask import docs from wqflask import news +from wqflask.submit_bnw import get_bnw_input from base.data_set import DataSet # Used by YAML in marker_regression from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data @@ -760,6 +761,11 @@ def corr_scatter_plot_page(): indent=" ") return render_template("corr_scatterplot.html", **template_vars.__dict__) +@app.route("/submit_bnw", methods=('POST',)) +def submit_bnw(): + logger.error(request.url) + template_vars = get_bnw_input(request.form) + return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) # Todo: Can we simplify this? -Sam def sharing_info_page(): |