diff options
| -rw-r--r-- | wqflask/base/data_set.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 42 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 41 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/admin/manage_user.html | 79 |
4 files changed, 142 insertions, 23 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 07704e4c..295f5c48 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -152,7 +152,8 @@ Publish or ProbeSet. E.g. if t in ['pheno', 'other_pheno']: name = name.replace("Publish", "") - if bool(len(g.db.execute(sql_query_mapping[t].format(name)))): + + if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())): self.datasets[name] = dataset_name_mapping[t] self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) return True diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 189c1985..78b1f7b0 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -37,6 +37,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") if control_marker != "" and do_control == "true": opt_list.append("-c " + control_marker) + if manhattan_plot != True: + opt_list.append("--interval 1") reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), genofile_name, @@ -85,9 +87,17 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): p_values = [] marker_obs = [] + only_cm = False + only_mb = False + with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, gwa_filename)) as output_file: for line in output_file: if line.startswith("ID\t"): + if len(line.split("\t")) < 8: + if 'cM' in line.split("\t"): + only_cm = True + else: + only_mb = True continue else: marker = {} @@ -96,16 +106,30 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): marker['chr'] = int(line.split("\t")[2]) except: marker['chr'] = line.split("\t")[2] - marker['cM'] = float(line.split("\t")[3]) - if float(line.split("\t")[4]) > 1000: - marker['Mb'] = float(line.split("\t")[4])/1000000 + if only_cm or only_mb: + if only_cm: + marker['cM'] = float(line.split("\t")[3]) + else: + if float(line.split("\t")[3]) > 1000: + marker['Mb'] = float(line.split("\t")[3])/1000000 + else: + marker['Mb'] = float(line.split("\t")[3]) + if float(line.split("\t")[6]) != 1: + marker['p_value'] = float(line.split("\t")[6]) + marker['lrs_value'] = float(line.split("\t")[4]) + marker['lod_score'] = marker['lrs_value'] / 4.61 + marker['additive'] = float(line.split("\t")[5]) else: - marker['Mb'] = float(line.split("\t")[4]) - if float(line.split("\t")[7]) != 1: - marker['p_value'] = float(line.split("\t")[7]) - marker['lrs_value'] = float(line.split("\t")[5]) - marker['lod_score'] = marker['lrs_value'] / 4.61 - marker['additive'] = float(line.split("\t")[6]) + marker['cM'] = float(line.split("\t")[3]) + if float(line.split("\t")[4]) > 1000: + marker['Mb'] = float(line.split("\t")[4])/1000000 + else: + marker['Mb'] = float(line.split("\t")[4]) + if float(line.split("\t")[7]) != 1: + marker['p_value'] = float(line.split("\t")[7]) + marker['lrs_value'] = float(line.split("\t")[5]) + marker['lod_score'] = marker['lrs_value'] / 4.61 + marker['additive'] = float(line.split("\t")[6]) marker_obs.append(marker) #ZS: Results have to be reordered because the new reaper returns results sorted alphabetically by chr for some reason, resulting in chr 1 being followed by 10, etc diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index 7ae84b16..c606cf53 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -372,10 +372,15 @@ class RunMapping(object): self.annotations_for_browser = [] highest_chr = 1 #This is needed in order to convert the highest chr to X/Y for marker in results: + if 'Mb' in marker: + this_ps = marker['Mb']*1000000 + else: + this_ps = marker['cM']*1000000 + browser_marker = dict( chr = str(marker['chr']), rs = marker['name'], - ps = marker['Mb']*1000000, + ps = this_ps, url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" ) @@ -384,7 +389,7 @@ class RunMapping(object): name = str(marker['name']), chr = str(marker['chr']), rs = marker['name'], - pos = marker['Mb']*1000000, + pos = this_ps, url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno" ) else: @@ -392,7 +397,7 @@ class RunMapping(object): name = str(marker['name']), chr = str(marker['chr']), rs = marker['name'], - pos = marker['Mb']*1000000 + pos = this_ps ) #if 'p_value' in marker: # logger.debug("P EXISTS:", marker['p_value']) @@ -531,10 +536,10 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write("\n") output_file.write("Name,Chr,") if score_type.lower() == "-log(p)": - score_type = "'-log(p)" - if mapping_scale == "physic": + score_type = "-log(p)" + if 'Mb' in markers[0]: output_file.write("Mb," + score_type) - else: + if 'cM' in markers[0]: output_file.write("Cm," + score_type) if "additive" in list(markers[0].keys()): output_file.write(",Additive") @@ -542,8 +547,12 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, output_file.write(",Dominance") output_file.write("\n") for i, marker in enumerate(markers): - output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",") - if "lod_score" in list(marker.keys()): + output_file.write(marker['name'] + "," + str(marker['chr']) + ",") + if 'Mb' in marker: + output_file.write(str(marker['Mb']) + ",") + if 'cM' in marker: + output_file.write(str(marker['cM']) + ",") + if "lod_score" in marker.keys(): output_file.write(str(marker['lod_score'])) else: output_file.write(str(marker['lrs_value'])) @@ -667,16 +676,22 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results): except: chr_as_num = 20 if chr_as_num > this_chr or i == (len(qtl_results) - 1): - chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)}) - this_chr = chr_as_num - highest_pos = 0 + if i == (len(qtl_results) - 1): + if mapping_method == "reaper": + highest_pos = float(result['cM']) * 1000000 + else: + highest_pos = float(result['Mb']) * 1000000 + chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)}) + else: + chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)}) + this_chr = chr_as_num else: if mapping_method == "reaper": if float(result['cM']) > highest_pos: - highest_pos = float(result['cM']) + highest_pos = float(result['cM']) * 1000000 else: if float(result['Mb']) > highest_pos: - highest_pos = float(result['Mb']) + highest_pos = float(result['Mb']) * 1000000 return chr_lengths diff --git a/wqflask/wqflask/templates/admin/manage_user.html b/wqflask/wqflask/templates/admin/manage_user.html new file mode 100644 index 00000000..7afe075f --- /dev/null +++ b/wqflask/wqflask/templates/admin/manage_user.html @@ -0,0 +1,79 @@ +{% extends "base.html" %} +{% block title %}View and Edit Group{% endblock %} +{% block css %} + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> + <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> +{% endblock %} +{% block content %} +<!-- Start of body --> + <div class="container"> + {% if 'full_name' in user_details %} + <div class="page-header"> + <h1>User details for: {{ user_details.full_name }}</h1> + </div> + {% endif %} + <form id="user_form" action="/user/manage" method="POST"> + <div class="row"> + <div id="user_info_div" class="col-xs-8" style="margin-right: 30px; min-width: 800px; max-width: 1000px;"> + <div class="form-horizontal"> + <div class="form-group"> + <label for="email_address" style="text-align: left;" class="col-xs-2">Email Address:</label> + <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls"> + <span id="email_address">{% if 'email_address' in user_details %}{{ user_details.email_address }}{% else %}N/A{% endif %}</span> + </div> + </div> + <div class="form-group"> + <label for="full_name" style="text-align: left;" class="col-xs-2">User Name:</label> + <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls"> + <span id="full_name" class="old_user_attribute">{% if 'full_name' in user_details %}{{ user_details.full_name }}{% else %}N/A{% endif %}</span> + <input type="text" name="new_full_name" style="display: none; width: 500px;" class="form-control new_user_attribute" placeholder="{% if 'full_name' in user_details %}{{ user_details.full_name }}{% else %}N/A{% endif %}"> + </div> + </div> + <div class="form-group"> + <label for="organization" style="text-align: left;" class="col-xs-2">Organization:</label> + <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls"> + <span id="organization" class="old_user_attribute">{% if 'organization' in user_details %}{{ user_details.organization }}{% else %}N/A{% endif %}</span> + <input type="text" name="new_organization" style="display: none; width: 500px;" class="form-control new_user_attribute" placeholder="{% if 'organization' in user_details %}{{ user_details.organization }}{% else %}N/A{% endif %}"> + </div> + </div> + <div class="form-group"> + <label for="change_user_details" style="text-align: left;" class="col-xs-2"></label> + <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls"> + <input type="button" id="change_user_details" value="Change Details"> + <input type="button" id="save_changes" value="Save Changes" style="display: none;"> + </div> + </div> + </div> + </div> + </div> + </form> + </div> + +<!-- End of body --> + +{% endblock %} + +{% block js %} + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> + + <script type="text/javascript" charset="utf-8"> + $(document).ready( function () { + $('#change_user_details').click(function(){ + $('.new_user_attribute').css("display", "inline-block"); + $('.old_user_attribute').css("display", "none"); + $('#change_user_details').css("display", "none"); + $('#save_changes').css("display", "inline-block"); + }); + + $('#save_changes').click(function(){ + $('.new_user_attribute').each(function(){ + if ($(this).val() == ""){ + $(this).val($(this).attr("placeholder")) + } + }); + $('#user_form').submit(); + }); + }); + </script> +{% endblock %} |