diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 36 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 13 |
4 files changed, 59 insertions, 0 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 9f2f06f3..9e01be3e 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -7,6 +7,7 @@ from pprint import pformat as pf import string import math +import random import sys import datetime import os @@ -30,6 +31,7 @@ from flask import Flask, g from base.trait import GeneralTrait from base import data_set from base import species +from base import webqtlConfig from utility import webqtlUtil from utility import helper_functions from utility import Plot, Bunch @@ -78,6 +80,12 @@ class MarkerRegression(object): self.vals.append(value) self.mapping_method = start_vars['method'] + if "results_path" in start_vars: + self.mapping_results_path = start_vars['results_path'] + else: + mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename) + if start_vars['manhattan_plot'] == "True": self.manhattan_plot = True else: @@ -269,6 +277,8 @@ class MarkerRegression(object): if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()): self.qtl_results.append(marker) + export_mapping_results(self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type) + self.trimmed_markers = trim_markers_for_table(results) if self.mapping_method != "gemma": @@ -598,6 +608,32 @@ def create_snp_iterator_file(group): with gzip.open(snp_file_base, "wb") as fh: pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL) +def export_mapping_results(markers, results_path, mapping_scale, score_type): + with open(results_path, "w+") as output_file: + output_file.write("Name\tChr\t") + if mapping_scale == "physic": + output_file.write("Mb\t" + score_type) + else: + output_file.write("Cm\t" + score_type) + if "additive" in markers[0].keys(): + output_file.write("\tAdditive") + if "dominance" in markers[0].keys(): + output_file.write("\tDominance") + output_file.write("\n") + for i, marker in enumerate(markers): + logger.debug("THE MARKER:", marker) + output_file.write(marker['name'] + "\t" + str(marker['chr']) + "\t" + str(marker['Mb']) + "\t") + if "lod_score" in marker.keys(): + output_file.write(str(marker['lod_score'])) + else: + output_file.write(str(marker['lrs_value'])) + if "additive" in marker.keys(): + output_file.write("\t" + str(marker['additive'])) + if "dominance" in marker.keys(): + output_file.write("\t" + str(marker['dominance'])) + if i < (len(markers) - 1): + output_file.write("\n") + def trim_markers_for_table(markers): num_markers = len(markers) diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index a26d1426..ff1fb492 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -178,6 +178,7 @@ class MarkerRegression(object): self.samples = start_vars['samples'] self.vals = start_vars['vals'] self.mapping_method = start_vars['mapping_method'] + self.mapping_results_path = start_vars['mapping_results_path'] if self.mapping_method == "rqtl_geno": self.mapmethod_rqtl_geno = start_vars['method'] self.mapmodel_rqtl_geno = start_vars['model'] diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 5c457275..d13c68cd 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -15,6 +15,7 @@ <input type="hidden" name="trait_id" value="{{ this_trait.name }}"> <input type="hidden" name="dataset" value="{{ dataset.name }}"> <input type="hidden" name="genofile" value="{{ genofile_string }}"> + <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> {% for sample in samples %} <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}"> @@ -46,6 +47,9 @@ {% if genofile_string is defined %} <b>Genotypes:</b> {{ genofile_string.split(":")[1] }} {% endif %} + <br> + <br> + <a href="javascript:export_mapping_results();" target="_blank" >Download Full Results</a> </div> <div id="gn1_map_options" class="col-xs-5" style="outline: 3px double #AAAAAA; padding: 10px; margin: 10px;"> <div class="col-xs-8" style="padding: 0px;"> @@ -407,6 +411,11 @@ } {% endif %} + export_mapping_results = function() { + $('#marker_regression_form').attr('action', '/export_mapping_results'); + return $('#marker_regression_form').submit(); + } + </script> {% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 174bf1e4..40806450 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -557,6 +557,7 @@ def marker_regression_page(): 'trait_id', 'dataset', 'method', + 'mapping_results_path', 'trimmed_markers', 'selected_chr', 'chromosomes', @@ -672,6 +673,18 @@ def marker_regression_page(): return rendered_template +@app.route("/export_mapping_results", methods = ('POST',)) +def export_mapping_results(): + logger.info("request.form:", request.form) + logger.error(request.url) + file_path = request.form.get("results_path") + results_csv = open(file_path, "r").read() + response = Response(results_csv, + mimetype='text/csv', + headers={"Content-Disposition":"attachment;filename=mapping_results.csv"}) + + return response + @app.route("/export", methods = ('POST',)) def export(): |