From d96fb158199c298494a7b15fb0edd63a937fd3cf Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 25 Aug 2020 16:06:30 -0500 Subject: This should fix an issue where the new qtlreaper wouldn't work properlty with genotypes that only have cM positions * wqflask/wqflask/marker_regression/qtlreaper_mapping.py - parse_reaper_output is changed to check if cM and Mb exist in output when creating marker obs * wqflask/wqflask/marker_regression/run_mapping.py - Changed export_mapping_results to properly deal with all combinations of cM and Mb positions (both and either/or) --- .../wqflask/marker_regression/qtlreaper_mapping.py | 42 +++++++++++++++++----- wqflask/wqflask/marker_regression/run_mapping.py | 39 +++++++++++++------- 2 files changed, 60 insertions(+), 21 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 0c560582..6b4c05ea 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 c9d10f7c..9bde343c 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -374,10 +374,15 @@ 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" ) @@ -386,7 +391,7 @@ 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: @@ -394,7 +399,7 @@ 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']) @@ -533,10 +538,10 @@ 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 markers[0].keys(): output_file.write(",Additive") @@ -544,7 +549,11 @@ 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']) + ",") + 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: @@ -669,16 +678,22 @@ 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 -- cgit v1.2.3 From 301bdd2f43de9121cd040dc6eab82a51eafae92f Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 25 Aug 2020 18:35:44 -0500 Subject: Fixed issue in DatasetType that caused an error when trying to load new datasets * wqflask/base/data_set.py - Added fetchone() to g.db.execute() which is what was causing the error --- wqflask/base/data_set.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index cfba9104..afffe780 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 -- cgit v1.2.3 From 433b41086d3f61a94778d7b244c0d0276794e59e Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 27 Aug 2020 15:07:43 -0500 Subject: Added manager_user.html because it was missing from git --- wqflask/wqflask/templates/admin/manage_user.html | 79 ++++++++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 wqflask/wqflask/templates/admin/manage_user.html (limited to 'wqflask') 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 %} + + + +{% endblock %} +{% block content %} + +
+ {% if 'full_name' in user_details %} +
+

User details for: {{ user_details.full_name }}

+
+ {% endif %} +
+
+
+
+
+ +
+ {% if 'email_address' in user_details %}{{ user_details.email_address }}{% else %}N/A{% endif %} +
+
+
+ +
+ {% if 'full_name' in user_details %}{{ user_details.full_name }}{% else %}N/A{% endif %} + +
+
+
+ +
+ {% if 'organization' in user_details %}{{ user_details.organization }}{% else %}N/A{% endif %} + +
+
+
+ +
+ + +
+
+
+
+
+
+
+ + + +{% endblock %} + +{% block js %} + + + +{% endblock %} -- cgit v1.2.3