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-rw-r--r--wqflask/base/webqtlConfig.py4
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py239
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py59
-rw-r--r--wqflask/utility/tools.py12
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py151
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py5
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py19
-rw-r--r--wqflask/wqflask/network_graph/network_graph.py12
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py6
-rw-r--r--wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js106
-rw-r--r--wqflask/wqflask/static/new/javascript/lodheatmap.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/network_graph.js4
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js23
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js15
-rw-r--r--wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css12
-rw-r--r--wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css6
-rw-r--r--wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css2
-rw-r--r--wqflask/wqflask/templates/collections/list.html5
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html4
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html1
-rw-r--r--wqflask/wqflask/templates/search_result_page.html2
-rw-r--r--wqflask/wqflask/templates/show_trait.html1
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html74
-rw-r--r--wqflask/wqflask/views.py2
25 files changed, 574 insertions, 194 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index e5f10edf..c3f1e76a 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -70,8 +70,8 @@ assert_writable_dir(TMPDIR)
CACHEDIR = mk_dir(TMPDIR+'/cache/')
# We can no longer write into the git tree:
-GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'/generated/')
-GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/')
+GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'generated/')
+GENERATED_TEXT_DIR = mk_dir(TMPDIR+'generated_text/')
# Make sure we have permissions to access these
assert_writable_dir(CACHEDIR)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
new file mode 100644
index 00000000..05006d5c
--- /dev/null
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -0,0 +1,239 @@
+#!/usr/bin/python
+
+"""
+Convert .geno files to json
+
+This file goes through all of the genofiles in the genofile directory (.geno)
+and converts them to json files that are used when running the marker regression
+code
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+import os
+import glob
+import traceback
+import gzip
+
+#import numpy as np
+#from pyLMM import lmm
+
+import simplejson as json
+
+from pprint import pformat as pf
+
+class EmptyConfigurations(Exception): pass
+
+
+
+class Marker(object):
+ def __init__(self):
+ self.name = None
+ self.chr = None
+ self.cM = None
+ self.Mb = None
+ self.genotypes = []
+
+class ConvertGenoFile(object):
+
+ def __init__(self, input_file, output_files):
+
+ self.input_file = input_file
+ self.output_files = output_files
+
+ self.mb_exists = False
+ self.cm_exists = False
+ self.markers = []
+
+ self.latest_row_pos = None
+ self.latest_col_pos = None
+
+ self.latest_row_value = None
+ self.latest_col_value = None
+
+ def convert(self):
+
+ self.haplotype_notation = {
+ '@mat': "1",
+ '@pat': "0",
+ '@het': "0.5",
+ '@unk': "NA"
+ }
+
+ self.configurations = {}
+ #self.skipped_cols = 3
+
+ #if self.input_file.endswith(".geno.gz"):
+ # print("self.input_file: ", self.input_file)
+ # self.input_fh = gzip.open(self.input_file)
+ #else:
+ self.input_fh = open(self.input_file)
+
+ with open(self.output_files[0], "w") as self.geno_fh:
+ #if self.file_type == "geno":
+ self.process_csv()
+ #elif self.file_type == "snps":
+ # self.process_snps_file()
+
+
+ def process_csv(self):
+ for row_count, row in enumerate(self.process_rows()):
+ row_items = row.split("\t")
+
+ this_marker = Marker()
+ this_marker.name = row_items[1]
+ this_marker.chr = row_items[0]
+ if self.cm_exists and self.mb_exists:
+ this_marker.cM = row_items[2]
+ this_marker.Mb = row_items[3]
+ genotypes = row_items[4:]
+ elif self.cm_exists:
+ this_marker.cM = row_items[2]
+ genotypes = row_items[3:]
+ elif self.mb_exists:
+ this_marker.Mb = row_items[2]
+ genotypes = row_items[3:]
+ else:
+ genotypes = row_items[2:]
+ for item_count, genotype in enumerate(genotypes):
+ if genotype.upper().strip() in self.configurations:
+ this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
+ else:
+ this_marker.genotypes.append("NA")
+
+ #print("this_marker is:", pf(this_marker.__dict__))
+ #if this_marker.chr == "14":
+ self.markers.append(this_marker.__dict__)
+
+ self.write_to_bimbam()
+
+ # with open(self.output_file, 'w') as fh:
+ # json.dump(self.markers, fh, indent=" ", sort_keys=True)
+
+ # print('configurations:', str(configurations))
+ #self.latest_col_pos = item_count + self.skipped_cols
+ #self.latest_col_value = item
+
+ #if item_count != 0:
+ # self.output_fh.write(" ")
+ #self.output_fh.write(self.configurations[item.upper()])
+
+ #self.output_fh.write("\n")
+
+ def write_to_bimbam(self):
+ with open(self.output_files[0], "w") as geno_fh:
+ # geno_fh.write(str(len(self.sample_list)) + "\n")
+ # geno_fh.write("2\n")
+ # geno_fh.write("IND")
+ # for sample in self.sample_list:
+ # geno_fh.write(" " + sample)
+ # geno_fh.write("\n")
+ for marker in self.markers:
+ geno_fh.write(marker['name'])
+ geno_fh.write(", X, Y")
+ geno_fh.write(", " + ", ".join(marker['genotypes']))
+ geno_fh.write("\n")
+
+ #pheno_fh = open(self.output_files[1], 'w')
+ with open(self.output_files[1], "w") as pheno_fh:
+ for sample in self.sample_list:
+ pheno_fh.write("1\n")
+
+ with open(self.output_files[2], "w") as snp_fh:
+ for marker in self.markers:
+ if self.mb_exists:
+ snp_fh.write(marker['name'] +", " + str(int(float(marker['Mb'])*1000000)) + ", " + marker['chr'] + "\n")
+ else:
+ snp_fh.write(marker['name'] +", " + str(int(float(marker['cM'])*1000000)) + ", " + marker['chr'] + "\n")
+
+
+ def get_sample_list(self, row_contents):
+ self.sample_list = []
+ if self.mb_exists:
+ if self.cm_exists:
+ self.sample_list = row_contents[4:]
+ else:
+ self.sample_list = row_contents[3:]
+ else:
+ if self.cm_exists:
+ self.sample_list = row_contents[3:]
+ else:
+ self.sample_list = row_contents[2:]
+
+ def process_rows(self):
+ for self.latest_row_pos, row in enumerate(self.input_fh):
+ #if self.input_file.endswith(".geno.gz"):
+ # print("row: ", row)
+ self.latest_row_value = row
+ # Take care of headers
+ if not row.strip():
+ continue
+ if row.startswith('#'):
+ continue
+ if row.startswith('Chr'):
+ if 'Mb' in row.split():
+ self.mb_exists = True
+ if 'cM' in row.split():
+ self.cm_exists = True
+ self.get_sample_list(row.split())
+ continue
+ if row.startswith('@'):
+ key, _separater, value = row.partition(':')
+ key = key.strip()
+ value = value.strip()
+ if key in self.haplotype_notation:
+ self.configurations[value] = self.haplotype_notation[key]
+ continue
+ if not len(self.configurations):
+ raise EmptyConfigurations
+ yield row
+
+ @classmethod
+ def process_all(cls, old_directory, new_directory):
+ os.chdir(old_directory)
+ for input_file in glob.glob("*"):
+ if not input_file.endswith(('geno', '.geno.gz')):
+ continue
+ group_name = ".".join(input_file.split('.')[:-1])
+ geno_output_file = os.path.join(new_directory, group_name + "_geno.txt")
+ pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt")
+ snp_output_file = os.path.join(new_directory, group_name + "_snps.txt")
+ output_files = [geno_output_file, pheno_output_file, snp_output_file]
+ print("%s -> %s" % (
+ os.path.join(old_directory, input_file), geno_output_file))
+ convertob = ConvertGenoFile(input_file, output_files)
+ try:
+ convertob.convert()
+ except EmptyConfigurations as why:
+ print(" No config info? Continuing...")
+ #excepted = True
+ continue
+ except Exception as why:
+
+ print(" Exception:", why)
+ print(traceback.print_exc())
+ print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos,
+ convertob.latest_col_pos))
+ print(" Column is:", convertob.latest_col_value)
+ print(" Row is:", convertob.latest_row_value)
+ break
+
+ #def process_snps_file(cls, snps_file, new_directory):
+ # output_file = os.path.join(new_directory, "mouse_families.json")
+ # print("%s -> %s" % (snps_file, output_file))
+ # convertob = ConvertGenoFile(input_file, output_file)
+
+
+if __name__=="__main__":
+ Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
+ New_Geno_Directory = """/home/zas1024/genotype_files/genotype/bimbam/"""
+ #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
+ #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
+ #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
+ #convertob.convert()
+ ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
+ #ConvertGenoFiles(Geno_Directory)
+
+ #process_csv(Input_File, Output_File) \ No newline at end of file
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
new file mode 100644
index 00000000..f322341d
--- /dev/null
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -0,0 +1,59 @@
+#!/usr/bin/python
+
+"""
+Generate relatedness matrix files for GEMMA from BIMBAM genotype/phenotype files
+
+This file goes through all of the BIMBAM files in the bimbam diretory
+and uses GEMMA to generate their corresponding kinship/relatedness matrix file
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+import os
+import glob
+
+class GenerateKinshipMatrices(object):
+ def __init__(self, group_name, geno_file, pheno_file):
+ self.group_name = group_name
+ self.geno_file = geno_file
+ self.pheno_file = pheno_file
+
+ def generate_kinship(self):
+ gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + " -p " + self.pheno_file + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
+ print("command:", gemma_command)
+ os.system(gemma_command)
+
+ @classmethod
+ def process_all(self, geno_dir, bimbam_dir):
+ os.chdir(geno_dir)
+ for input_file in glob.glob("*"):
+ if not input_file.endswith(('geno', '.geno.gz')):
+ continue
+ group_name = ".".join(input_file.split('.')[:-1])
+ geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt")
+ pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt")
+ convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file)
+ try:
+ convertob.generate_kinship()
+ except EmptyConfigurations as why:
+ print(" No config info? Continuing...")
+ continue
+ except Exception as why:
+
+ print(" Exception:", why)
+ print(traceback.print_exc())
+ print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos,
+ convertob.latest_col_pos))
+ print(" Column is:", convertob.latest_col_value)
+ print(" Row is:", convertob.latest_row_value)
+ break
+
+
+if __name__=="__main__":
+ Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
+ Bimbam_Directory = """/home/zas1024/genotype_files/genotype/bimbam/"""
+ GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
+
+ #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 867bc5c8..c5685cdd 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -113,6 +113,9 @@ def pylmm_command(guess=None):
def gemma_command(guess=None):
return assert_bin(get_setting("GEMMA_COMMAND",guess))
+def gemma_wrapper_command(guess=None):
+ return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess))
+
def plink_command(guess=None):
return assert_bin(get_setting("PLINK_COMMAND",guess))
@@ -240,10 +243,11 @@ JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
JS_GN_PATH = get_setting('JS_GN_PATH')
# assert_dir(JS_GN_PATH)
-PYLMM_COMMAND = pylmm_command()
-GEMMA_COMMAND = gemma_command()
-PLINK_COMMAND = plink_command()
-TEMPDIR = tempdir() # defaults to UNIX TMPDIR
+PYLMM_COMMAND = pylmm_command()
+GEMMA_COMMAND = gemma_command()
+GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
+PLINK_COMMAND = plink_command()
+TEMPDIR = tempdir() # defaults to UNIX TMPDIR
# ---- Handle specific JS modules
JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher"))
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 6e2cb972..31e94266 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,24 +1,75 @@
import os, math
from base import webqtlConfig
+from base.trait import GeneralTrait
+from base.data_set import create_dataset
from utility.tools import flat_files, GEMMA_COMMAND
-def run_gemma(this_dataset, samples, vals):
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+def run_gemma(this_dataset, samples, vals, covariates, method):
"""Generates p-values for each marker using GEMMA"""
print("INSIDE GEMMA_MAPPING")
- gen_pheno_txt_file(this_dataset, vals)
+ gen_pheno_txt_file(this_dataset, vals, method)
+
+ if not os.path.isfile("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name)):
+ open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name), "w+")
- # use GEMMA_RUN in the next one, create a unique temp file
+ logger.debug("COVARIATES_GEMMA:", covariates)
- gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -outdir %s -o %s_output' % (flat_files('mapping'),
- this_dataset.group.name,
- flat_files('mapping'),
- this_dataset.group.name,
- webqtlConfig.GENERATED_IMAGE_DIR,
- this_dataset.group.name)
- print("gemma_command:" + gemma_command)
+ if covariates != "":
+ gen_covariates_file(this_dataset, covariates)
+ if method == "gemma":
+ #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -o %s_output' % (flat_files('mapping'),
+ gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
+ this_dataset.group.name,
+ flat_files('mapping'),
+ this_dataset.group.name,
+ flat_files('mapping'),
+ this_dataset.group.name,
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
+ # use GEMMA_RUN in the next one, create a unique temp file
+ else:
+ logger.debug("FLAT FILES:", flat_files('mapping'))
+ #gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -o %s_output' % (flat_files('genotype/bimbam'),
+ gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('mapping'),
+ this_dataset.group.name,
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
+ else:
+ if method == "gemma":
+ #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('mapping'),
+ gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -outdir %s -o %s_output' % (flat_files('mapping'),
+ this_dataset.group.name,
+ flat_files('mapping'),
+ this_dataset.group.name,
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
+ else:
+ #gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('genotype/bimbam'),
+ gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
+ logger.debug("gemma_command:" + gemma_command)
os.system(gemma_command)
@@ -26,27 +77,70 @@ def run_gemma(this_dataset, samples, vals):
return marker_obs
-def gen_pheno_txt_file(this_dataset, vals):
+def gen_pheno_txt_file(this_dataset, vals, method):
"""Generates phenotype file for GEMMA"""
- current_file_data = []
- with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile:
- for i, line in enumerate(outfile):
- split_line = line.split()
- current_file_data.append(split_line)
-
- with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
- for i, line in enumerate(current_file_data):
- if vals[i] == "x":
- this_val = -9
+ if method == "gemma":
+ current_file_data = []
+ with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile:
+ for i, line in enumerate(outfile):
+ split_line = line.split()
+ current_file_data.append(split_line)
+
+ with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
+ for i, line in enumerate(current_file_data):
+ if vals[i] == "x":
+ this_val = -9
+ else:
+ this_val = vals[i]
+ outfile.write("0" + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
+ else:
+ current_file_data = []
+ with open("{}/{}_pheno.txt".format(flat_files('genotype/bimbam'), this_dataset.group.name), "w") as outfile:
+ for value in vals:
+ if value == "x":
+ outfile.write("NA\n")
+ else:
+ outfile.write(value + "\n")
+
+def gen_covariates_file(this_dataset, covariates):
+ covariate_list = covariates.split(",")
+ covariate_data_object = []
+ for covariate in covariate_list:
+ this_covariate_data = []
+ trait_name = covariate.split(":")[0]
+ dataset_ob = create_dataset(covariate.split(":")[1])
+ trait_ob = GeneralTrait(dataset=dataset_ob,
+ name=trait_name,
+ cellid=None)
+
+ #trait_samples = this_dataset.group.all_samples_ordered()
+ this_dataset.group.get_samplelist()
+ trait_samples = this_dataset.group.samplelist
+ logger.debug("SAMPLES:", trait_samples)
+ trait_sample_data = trait_ob.data
+ logger.debug("SAMPLE DATA:", trait_sample_data)
+ for index, sample in enumerate(trait_samples):
+ if sample in trait_sample_data:
+ sample_value = trait_sample_data[sample].value
+ this_covariate_data.append(sample_value)
else:
- this_val = vals[i]
- outfile.write("0" + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
+ this_covariate_data.append("-9")
+ covariate_data_object.append(this_covariate_data)
+
+ with open("{}/{}_covariates.txt".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
+ for i in range(len(covariate_data_object[0])):
+ for this_covariate in covariate_data_object:
+ outfile.write(str(this_covariate[i]) + "\t")
+ outfile.write("\n")
def parse_gemma_output(this_dataset):
included_markers = []
p_values = []
marker_obs = []
+ previous_chr = 0
+
+ #with open("/home/zas1024/gene/wqflask/output/{}_output.assoc.txt".format(this_dataset.group.name)) as output_file:
with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name)) as output_file:
for line in output_file:
if line.startswith("chr"):
@@ -54,7 +148,16 @@ def parse_gemma_output(this_dataset):
else:
marker = {}
marker['name'] = line.split("\t")[1]
- marker['chr'] = int(line.split("\t")[0])
+ if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
+ marker['chr'] = int(line.split("\t")[0])
+ else:
+ marker['chr'] = line.split("\t")[0]
+ # try:
+ # marker['chr'] = int(line.split("\t")[0])
+ # except:
+ # marker['chr'] = previous_chr + 1
+ # if marker['chr'] != previous_chr:
+ # previous_chr = marker['chr']
marker['Mb'] = float(line.split("\t")[2]) / 1000000
marker['p_value'] = float(line.split("\t")[10])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 60424468..55bbacac 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -92,6 +92,7 @@ class MarkerRegression(object):
self.num_perm = 0
self.perm_output = []
self.bootstrap_results = []
+ self.covariates = start_vars['covariates']
#ZS: This is passed to GN1 code for single chr mapping
self.selected_chr = -1
@@ -153,11 +154,11 @@ class MarkerRegression(object):
self.genofile_string = start_vars['genofile']
self.dataset.group.genofile = self.genofile_string.split(":")[0]
self.dataset.group.get_markers()
- if self.mapping_method == "gemma":
+ if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
self.score_type = "-log(p)"
self.manhattan_plot = True
with Bench("Running GEMMA"):
- marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals)
+ marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals, self.covariates, self.mapping_method)
results = marker_obs
elif self.mapping_method == "rqtl_plink":
results = self.run_rqtl_plink()
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 08332e7d..93d75a03 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -255,6 +255,8 @@ class MarkerRegression(object):
self.controlLocus = start_vars['control_marker']
else:
self.controlLocus = ""
+ if 'covariates' in start_vars.keys():
+ self.covariates = start_vars['covariates']
#try:
self.selectedChr = int(start_vars['selected_chr'])
@@ -1369,7 +1371,10 @@ class MarkerRegression(object):
#draw gray blocks for 3' and 5' UTR blocks
if cdsStart and cdsEnd:
-
+ logger.debug("txStart:", txStart)
+ logger.debug("cdsStart:", cdsStart)
+ logger.debug("txEnd:", txEnd)
+ logger.debug("cdsEnd:", cdsEnd)
utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset
utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset
if (utrStartPix < xLeftOffset):
@@ -1380,9 +1385,10 @@ class MarkerRegression(object):
utrEndPix = xLeftOffset + plotWidth
if (utrStartPix > xLeftOffset + plotWidth):
utrStartPix = xLeftOffset + plotWidth
- canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
+ #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
- if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+ #if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+ if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
if strand == "-":
labelText = "3'"
else:
@@ -1401,10 +1407,11 @@ class MarkerRegression(object):
utrEndPix = xLeftOffset + plotWidth
if (utrStartPix > xLeftOffset + plotWidth):
utrStartPix = xLeftOffset + plotWidth
- canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
+ #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
- if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
- if tstrand == "-":
+ #if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+ if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
+ if strand == "-":
labelText = "5'"
else:
labelText = "3'"
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 7eb5be61..b42904a4 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -182,24 +182,18 @@ class NetworkGraph(object):
self.edges_list.append(edge_dict)
if trait_db[1].type == "ProbeSet":
- node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
- 'name' : str(this_trait.name),
- 'dataset' : str(this_trait.dataset.name),
+ node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
'label' : this_trait.symbol,
'symbol' : this_trait.symbol,
'geneid' : this_trait.geneid,
'omim' : this_trait.omim,
'max_corr' : max_corr } }
elif trait_db[1].type == "Publish":
- node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
- 'name' : str(this_trait.name),
- 'dataset' : str(this_trait.dataset.name),
+ node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
'label' : this_trait.name,
'max_corr' : max_corr } }
else:
- node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
- 'name' : str(this_trait.name),
- 'dataset' : str(this_trait.dataset.name),
+ node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
'label' : this_trait.name,
'max_corr' : max_corr } }
self.nodes_list.append(node_dict)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index b2dfc4ac..13ad4a8f 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -133,9 +133,9 @@ class ShowTrait(object):
self.sample_group_types = OrderedDict()
if len(self.sample_groups) > 1:
- self.sample_group_types['samples_primary'] = self.dataset.group.name + " Only"
- self.sample_group_types['samples_other'] = "Non-" + self.dataset.group.name
- self.sample_group_types['samples_all'] = "All Cases"
+ self.sample_group_types['samples_primary'] = self.dataset.group.name
+ self.sample_group_types['samples_other'] = "Other"
+ self.sample_group_types['samples_all'] = "All"
else:
self.sample_group_types['samples_primary'] = self.dataset.group.name
sample_lists = [group.sample_list for group in self.sample_groups]
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index c267b045..92e2b13b 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -2,8 +2,6 @@
var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, create_trait_data_csv, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click,
__indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
-console.log("before get_traits_from_collection");
-
collection_list = null;
this_trait_data = null;
@@ -25,109 +23,30 @@ collection_click = function() {
};
submit_click = function() {
- var all_vals, sample, samples, scatter_matrix, this_trait_vals, trait, trait_names, trait_vals_csv, traits, _i, _j, _len, _len1, _ref;
- selected_traits = {};
- traits = [];
+ var covariates_string = "";
$('#collections_holder').find('input[type=checkbox]:checked').each(function() {
- var this_dataset, this_trait, this_trait_url;
+ var this_dataset, this_trait;
this_trait = $(this).parents('tr').find('.trait').text();
console.log("this_trait is:", this_trait);
this_dataset = $(this).parents('tr').find('.dataset').text();
console.log("this_dataset is:", this_dataset);
- this_trait_url = "/trait/get_sample_data?trait=" + this_trait + "&dataset=" + this_dataset;
- return $.ajax({
- dataType: "json",
- url: this_trait_url,
- async: false,
- success: add_trait_data
- });
+ covariates_string += this_trait + ":" + this_dataset + ","
});
- console.log("SELECTED_TRAITS IS:", selected_traits);
- trait_names = [];
- samples = $('input[name=allsamples]').val().split(" ");
- all_vals = [];
- this_trait_vals = get_this_trait_vals(samples);
- all_vals.push(this_trait_vals);
- _ref = Object.keys(selected_traits);
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- trait = _ref[_i];
- trait_names.push(trait);
- this_trait_vals = [];
- for (_j = 0, _len1 = samples.length; _j < _len1; _j++) {
- sample = samples[_j];
- if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) {
- this_trait_vals.push(parseFloat(selected_traits[trait][sample]));
- } else {
- this_trait_vals.push(null);
- }
- }
- all_vals.push(this_trait_vals);
- }
- trait_vals_csv = create_trait_data_csv(selected_traits);
- scatter_matrix = new ScatterMatrix(trait_vals_csv);
- scatter_matrix.render();
- return $.colorbox.close();
-};
+ // Trim the last comma
+ covariates_string = covariates_string.substring(0, covariates_string.length - 1)
+ console.log("COVARIATES:", covariates_string)
-create_trait_data_csv = function(selected_traits) {
- var all_vals, index, sample, sample_vals, samples, this_trait_vals, trait, trait_names, trait_vals_csv, _i, _j, _k, _l, _len, _len1, _len2, _len3, _ref;
- trait_names = [];
- trait_names.push($('input[name=trait_id]').val());
- samples = $('input[name=allsamples]').val().split(" ");
- all_vals = [];
- this_trait_vals = get_this_trait_vals(samples);
- all_vals.push(this_trait_vals);
- _ref = Object.keys(selected_traits);
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- trait = _ref[_i];
- trait_names.push(trait);
- this_trait_vals = [];
- for (_j = 0, _len1 = samples.length; _j < _len1; _j++) {
- sample = samples[_j];
- if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) {
- this_trait_vals.push(parseFloat(selected_traits[trait][sample]));
- } else {
- this_trait_vals.push(null);
- }
- }
- all_vals.push(this_trait_vals);
- }
- console.log("all_vals:", all_vals);
- trait_vals_csv = trait_names.join(",");
- trait_vals_csv += "\n";
- for (index = _k = 0, _len2 = samples.length; _k < _len2; index = ++_k) {
- sample = samples[index];
- if (all_vals[0][index] === null) {
- continue;
- }
- sample_vals = [];
- for (_l = 0, _len3 = all_vals.length; _l < _len3; _l++) {
- trait = all_vals[_l];
- sample_vals.push(trait[index]);
- }
- trait_vals_csv += sample_vals.join(",");
- trait_vals_csv += "\n";
- }
- return trait_vals_csv;
+ $("input[name=covariates]").val(covariates_string)
+
+ return $.colorbox.close();
};
trait_click = function() {
var dataset, this_trait_url, trait;
- console.log("Clicking on:", $(this));
trait = $(this).parent().find('.trait').text();
dataset = $(this).parent().find('.dataset').text();
- console.log("BEFORE COVAR:", trait + ":" + dataset)
- $('input[name=covariates]').val(trait + ":" + dataset)
- console.log("AFTER COVAR:", $('input[name=covariates]').val())
+ $("input[name=covariates]").val(trait + ":" + dataset)
return $.colorbox.close();
- // this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
- // console.log("this_trait_url", this_trait_url);
- // $.ajax({
- // dataType: "json",
- // url: this_trait_url,
- // success: get_trait_data
- // });
- // return $.colorbox.close();
};
add_trait_data = function(trait_data, textStatus, jqXHR) {
@@ -140,9 +59,7 @@ add_trait_data = function(trait_data, textStatus, jqXHR) {
get_trait_data = function(trait_data, textStatus, jqXHR) {
var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len;
- console.log("trait:", trait_data[0]);
trait_sample_data = trait_data[1];
- console.log("trait_sample_data:", trait_sample_data);
samples = $('input[name=allsamples]').val().split(" ");
vals = [];
for (_i = 0, _len = samples.length; _i < _len; _i++) {
@@ -158,7 +75,6 @@ get_trait_data = function(trait_data, textStatus, jqXHR) {
}
$('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
this_trait_vals = get_this_trait_vals(samples);
- console.log("THE LENGTH IS:", $('input[name=vals]').length);
return color_by_trait(trait_sample_data);
};
@@ -174,7 +90,6 @@ get_this_trait_vals = function(samples) {
this_trait_vals.push(null);
}
}
- console.log("this_trait_vals:", this_trait_vals);
this_vals_json = '[' + this_trait_vals.toString() + ']';
return this_trait_vals;
};
@@ -231,7 +146,6 @@ back_to_collections = function() {
return $('#collections_holder').colorbox.resize();
};
-console.log("inside get_traits_from_collection");
$(".collection_line").on("click", collection_click);
$("#submit").on("click", submit_click);
$(".trait").on("click", trait_click);
diff --git a/wqflask/wqflask/static/new/javascript/lodheatmap.js b/wqflask/wqflask/static/new/javascript/lodheatmap.js
index f604cd10..965a1d53 100644
--- a/wqflask/wqflask/static/new/javascript/lodheatmap.js
+++ b/wqflask/wqflask/static/new/javascript/lodheatmap.js
@@ -20,7 +20,7 @@ lodheatmap = function() {
chrGap = 8;
titlepos = 20;
rectcolor = d3.rgb(230, 230, 230);
- colors = ["blue", "white", "crimson"];
+ colors = ["slateblue", "white", "red"];
title = "";
xlab = "Chromosome";
ylab = "";
diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js
index 03ef1c98..0129bcae 100644
--- a/wqflask/wqflask/static/new/javascript/network_graph.js
+++ b/wqflask/wqflask/static/new/javascript/network_graph.js
@@ -6,7 +6,7 @@ window.onload=function() {
container: $('#cytoscapeweb'), // container to render in
elements: elements_list,
-
+
style: [ // the stylesheet for the graph
{
selector: 'node',
@@ -82,7 +82,7 @@ window.onload=function() {
cy.nodes().qtip({
content: function(){
qtip_content = ''
- gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().name + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>'
+ gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>'
qtip_content += gn_link
if (typeof(this.data().geneid) !== 'undefined'){
ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>'
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index f232c6eb..f08965e9 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -74,11 +74,14 @@
return open_trait_selection();
};
})(this));
- d3.select("#select_covariate").on("click", (function(_this) {
+ d3.select("#select_covariates").on("click", (function(_this) {
return function() {
return open_covariate_selection();
};
})(this));
+ $("#remove_covariates").click(function () {
+ $("input[name=covariates]").val("")
+ });
d3.select("#clear_compare_trait").on("click", (function(_this) {
return function() {
return $('.scatter-matrix-container').remove();
@@ -101,15 +104,15 @@
})(this));
};
open_covariate_selection = function() {
- return $('#collections_holder').load('/collections/list?select_covariates #collections_list', (function(_this) {
+ return $('#collections_holder').load('/collections/list #collections_list', (function(_this) {
return function() {
$.colorbox({
inline: true,
href: "#collections_holder",
onComplete: function(){
- console.log("before get script")
+ console.log("before get cov script")
$.getScript("/static/new/javascript/get_covariates_from_collection.js");
- console.log("after get script")
+ console.log("after get cov script")
}
});
return $('a.collection_name').attr('onClick', 'return false');
@@ -199,16 +202,16 @@
};
make_table = function() {
var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
- header = "<thead><tr><th style=\"padding-left: 5px;\">Statistic</th>";
+ header = "<thead><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
_ref = js_data.sample_group_types;
for (key in _ref) {
if (!__hasProp.call(_ref, key)) continue;
value = _ref[key];
the_id = process_id("column", key);
if (Object.keys(_ref).length > 1) {
- header += "<th id=\"" + the_id + "\" style=\"padding-left: 5px;\">" + value + "</th>";
+ header += "<th id=\"" + the_id + "\" style=\"text-align: right; padding-left: 5px;\">" + value + "</th>";
} else {
- header += "<th id=\"" + the_id + "\" style=\"padding-left: 5px;\">Value</th>";
+ header += "<th id=\"" + the_id + "\" style=\"text-align: right; padding-left: 5px;\">Value</th>";
}
}
@@ -221,16 +224,16 @@
}
row_line = "<tr>";
if (row.url != null) {
- row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\" style=\"color: #000000;\">" + row.pretty + "</a></td>";
+ row_line += "<td id=\"" + row.vn + "\" align=\"right\"><a href=\"" + row.url + "\" style=\"color: #000000;\">" + row.pretty + "</a></td>";
} else {
- row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
+ row_line += "<td id=\"" + row.vn + "\" align=\"right\">" + row.pretty + "</td>";
}
_ref1 = js_data.sample_group_types;
for (key in _ref1) {
if (!__hasProp.call(_ref1, key)) continue;
value = _ref1[key];
the_id = process_id(key, row.vn);
- row_line += "<td id=\"" + the_id + "\">foo</td>";
+ row_line += "<td id=\"" + the_id + "\" align=\"right\">foo</td>";
}
row_line += "</tr>";
the_rows += row_line;
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index d6cd8134..e11aaf4a 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -237,6 +237,21 @@
};
})(this));
+ $("#gemma_bimbam_compute").on("click", (function(_this) {
+ return function() {
+ var form_data, url;
+ console.log("RUNNING GEMMA");
+ //$("#static_progress_bar_container").modal();
+ url = "/loading";
+ $('input[name=method]').val("gemma_bimbam");
+ $('input[name=maf]').val($('input[name=maf_gemma]').val());
+ form_data = $('#trait_data_form').serialize();
+ console.log("form_data is:", form_data);
+ return submit_special(url);
+ //return do_ajax_post(url, form_data);
+ };
+ })(this));
+
$("#interval_mapping_compute").on("click", (function(_this) {
return function() {
var form_data, url;
diff --git a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
index a5b9f09c..f376d15e 100644
--- a/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
+++ b/wqflask/wqflask/static/new/packages/DataTables/css/jquery.dataTables.css
@@ -80,7 +80,7 @@ table.dataTable tbody tr {
background-color: #ffffff;
}
table.dataTable tbody tr.selected {
- background-color: #abb9d3;
+ background-color: #ffee99;
}
table.dataTable tbody th,
table.dataTable tbody td {
@@ -111,13 +111,13 @@ table.dataTable.stripe tbody tr.odd, table.dataTable.display tbody tr.odd {
background-color: #f9f9f9;
}
table.dataTable.stripe tbody tr.odd.selected, table.dataTable.display tbody tr.odd.selected {
- background-color: #abb9d3;
+ background-color: #FFEE99;
}
table.dataTable.hover tbody tr:hover, table.dataTable.display tbody tr:hover {
background-color: whitesmoke;
}
table.dataTable.hover tbody tr:hover.selected, table.dataTable.display tbody tr:hover.selected {
- background-color: #a9b7d1;
+ background-color: #FFEE99;
}
table.dataTable.order-column tbody tr > .sorting_1,
table.dataTable.order-column tbody tr > .sorting_2,
@@ -143,7 +143,7 @@ table.dataTable.display tbody tr.odd > .sorting_3, table.dataTable.order-column.
background-color: whitesmoke;
}
table.dataTable.display tbody tr.odd.selected > .sorting_1, table.dataTable.order-column.stripe tbody tr.odd.selected > .sorting_1 {
- background-color: #a6b3cd;
+ background-color: #ffe047;
}
table.dataTable.display tbody tr.odd.selected > .sorting_2, table.dataTable.order-column.stripe tbody tr.odd.selected > .sorting_2 {
background-color: #a7b5ce;
@@ -161,7 +161,7 @@ table.dataTable.display tbody tr.even > .sorting_3, table.dataTable.order-column
background-color: #fdfdfd;
}
table.dataTable.display tbody tr.even.selected > .sorting_1, table.dataTable.order-column.stripe tbody tr.even.selected > .sorting_1 {
- background-color: #acbad4;
+ background-color: #ffe047;
}
table.dataTable.display tbody tr.even.selected > .sorting_2, table.dataTable.order-column.stripe tbody tr.even.selected > .sorting_2 {
background-color: #adbbd6;
@@ -179,7 +179,7 @@ table.dataTable.display tbody tr:hover > .sorting_3, table.dataTable.order-colum
background-color: #eeeeee;
}
table.dataTable.display tbody tr:hover.selected > .sorting_1, table.dataTable.order-column.hover tbody tr:hover.selected > .sorting_1 {
- background-color: #a1aec7;
+ background-color: #ffe047;
}
table.dataTable.display tbody tr:hover.selected > .sorting_2, table.dataTable.order-column.hover tbody tr:hover.selected > .sorting_2 {
background-color: #a2afc8;
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
index 91aaa98f..e6abe790 100644
--- a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
@@ -3803,7 +3803,7 @@ select[multiple].input-group-sm > .input-group-btn > .btn {
.nav-pills > li.active > a:hover,
.nav-pills > li.active > a:focus {
color: #fff;
- background-color: #428bca;
+ background-color: #3071a9; /* Tab cell background color */
}
.nav-stacked > li {
float: none;
@@ -4485,7 +4485,7 @@ fieldset[disabled] .navbar-inverse .btn-link:focus {
z-index: 2;
color: #fff;
cursor: default;
- background-color: #428bca;
+ background-color: #3071a9;
border-color: #428bca;
}
.pagination > .disabled > span,
@@ -4667,7 +4667,7 @@ a.badge:focus {
}
a.list-group-item.active > .badge,
.nav-pills > .active > a > .badge {
- color: #428bca;
+ color: #3071a9;
background-color: #fff;
}
.nav-pills > li > a > .badge {
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
index 9da73a8f..d352390f 100644
--- a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
@@ -97,7 +97,7 @@ body {
.navbar .navbar-nav .open .dropdown-menu > .active > a:hover,
.navbar .navbar-nav .open .dropdown-menu > .active > a:focus {
color: #fff !important;
- background-color: #428bca !important;
+ background-color: #3071a9 !important;
}
.navbar .navbar-nav .open .dropdown-menu > .disabled > a,
.navbar .navbar-nav .open .dropdown-menu > .disabled > a:hover,
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index cc60ecff..ad72052e 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -65,11 +65,6 @@
{% endfor %}
</tbody>
</table>
- {% if "color_by_trait" in params %}
- <script language="javascript" type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
- {% else %}
- <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
- {% endif %}
</div>
</div>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index c2f687fd..6f2ad0b8 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -27,8 +27,8 @@
<button class="btn btn-default" id="export_traits">Download CSV</button>
</form>
<br />
- <div style="width: 2000px;">
- <table width="2000px" id="trait_table" class="display dataTable nowrap" style="float: left;">
+ <div style="width: 100%;">
+ <table width="100%" id="trait_table" class="display dataTable nowrap" style="float: left;">
<thead>
<tr>
<th></th>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 5afd134a..c6c6bc23 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -27,6 +27,7 @@
<input type="hidden" name="num_bootstrap" value="{{ nboot }}">
<input type="hidden" name="do_control" value="{{ doControl }}">
<input type="hidden" name="control_marker" value="{{ controlLocus }}">
+ <input type="hidden" name="covariates" values="{{ covariates }}">
<input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}">
<input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}">
<input type="hidden" name="pair_scan" value="{{ pair_scan }}">
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 93e24cc7..9ad8a53e 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -234,6 +234,7 @@
"autoWidth": false,
"deferRender": true,
"bSortClasses": false,
+ "scrollX": true,
"scrollY": "600px",
"scrollCollapse": false,
"scroller": true,
@@ -306,6 +307,7 @@
"autoWidth": false,
"deferRender": true,
"bSortClasses": false,
+ "scrollY": "600px",
"scrollCollapse": false,
"scroller": false,
"paging": false,
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7c4dbc60..c2724fea 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -142,6 +142,7 @@
<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/compare_traits_scatterplot.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 0e15ce9c..c5f815ce 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -105,7 +105,7 @@
<div class="form-group">
<label for="corr_sample_method" class="col-xs-1 control-label"></label>
<div class="col-xs-4 controls">
- <button class="btn corr_compute submit_special btn-primary" data-url="/corr_compute" title="Compute Correlation">
+ <button class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index bded60d2..c24a5853 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -4,7 +4,6 @@
<div class="tabbable"> <!-- Only required for left/right tabs -->
<ul class="nav nav-pills">
- {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
{% if dataset.group.mapping_id == "1" %}
<li class="active">
<a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
@@ -15,12 +14,14 @@
<li>
<a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
</li>
+ <li>
+ <a href="#gemma" data-toggle="tab">GEMMA</a>
+ </li>
{% endif %}
- {# if use_plink_gemma #}
{% for mapping_method in dataset.group.mapping_names %}
{% if mapping_method == "GEMMA" %}
<li class="active">
- <a href="#gemma" data-toggle="tab">GEMMA</a>
+ <a href="#gemma_plink" data-toggle="tab">GEMMA</a>
</li>
{% elif mapping_method == "PLINK" %}
<li>
@@ -122,7 +123,7 @@
</div>
<div class="form-group">
<div style="padding-left:15px;" class="controls">
- <button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Interval Mapping">
+ <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
@@ -179,7 +180,7 @@
-->
<div class="form-group">
<div style="padding-left:15px;" class="controls">
- <button id="pylmm_compute" class="btn submit_special btn-primary" title="Compute Marker Regression">
+ <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
@@ -286,36 +287,75 @@
<div class="form-group">
<div style="padding-left:15px;" class="controls">
- <button id="rqtl_geno_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
<i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
</div>
</div>
</div>
+ <div class="tab-pane" id="gemma">
+ <div style="padding-top: 10px;" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
+ <div style="margin-left: 20px;" class="col-xs-3 controls">
+ <input name="maf_gemma" value="0.01" type="text" class="form-control">
+ </div>
+ </div>
+ </div>
+
+ <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <button type="button" id="select_covariates" class="btn btn-default">
+ Select Covariates
+ </button>
+ <button type="button" id="remove_covariates" class="btn btn-default">
+ Remove Covariates
+ </button>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <div class="col-xs-4 controls">
+ <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+ Compute
+ </button>
+ </div>
+ </div>
+ </div>
{% endif %}
- {# if use_plink_gemma #}
- {% if dataset.group.mapping_id == "2" or dataset.group.mapping_id == "4" %}
- <div class="tab-pane active" id="gemma">
- <div style="padding: 20px" class="form-horizontal">
+ {% for mapping_method in dataset.group.mapping_names %}
+ {% if mapping_method == "GEMMA" %}
+ <div class="tab-pane active" id="gemma_plink">
+ <div style="padding-top: 10px;" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="maf_gemma" class="col-xs-3 control-label">Minor allele threshold</label>
+ <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
<div style="margin-left: 20px;" class="col-xs-3 controls">
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
</div>
+ <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <button type="button" id="select_covariates" class="btn btn-default">
+ Select Covariates
+ </button>
+ <button type="button" id="remove_covariates" class="btn btn-default">
+ Remove Covariates
+ </button>
+ </div>
+ </div>
+
<div class="form-group">
- <label for="gemma_compute" class="col-xs-1 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="gemma_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <div class="col-xs-4 controls">
+ <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
</div>
</div>
</div>
- {% if dataset.group.mapping_id == "4" %}
+ {% elif mapping_method == "PLINK" %}
<div class="tab-pane" id="plink">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
@@ -329,14 +369,14 @@
<div class="form-group">
<label for="plink_compute" class="col-xs-1 control-label"></label>
<div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="plink_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <button id="plink_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
</div>
</div>
</div>
{% endif %}
- {% endif %}
+ {% endfor %}
</div>
</div>
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 83496000..2d4fd0f2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -514,6 +514,7 @@ def loading_page():
'bootCheck',
'bootstrap_results',
'LRSCheck',
+ 'covariates',
'maf',
'manhattan_plot',
'control_marker',
@@ -569,6 +570,7 @@ def marker_regression_page():
'bootCheck',
'bootstrap_results',
'LRSCheck',
+ 'covariates',
'maf',
'manhattan_plot',
'control_marker',