diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 221 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/parser.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/mapping_results.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_mapping_tools.html | 13 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
8 files changed, 147 insertions, 128 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index bc8f8fd9..41d5c9d0 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -154,6 +154,10 @@ class DisplayMappingResults(object): self.geno_db_exists = start_vars['geno_db_exists'] + self.first_run = True + if 'first_run' in start_vars: + self.first_run = start_vars['first_run'] + #Needing for form submission when doing single chr mapping or remapping after changing options self.samples = start_vars['samples'] self.vals = start_vars['vals'] @@ -226,6 +230,8 @@ class DisplayMappingResults(object): self.maf = start_vars['maf'] if 'use_loco' in start_vars.keys(): self.use_loco = start_vars['use_loco'] + if self.use_loco == "True": + self.gwa_filename = start_vars['gwa_filename'] self.selectedChr = int(start_vars['selected_chr']) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 9e92838e..0f37e711 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -12,7 +12,7 @@ GEMMAOPTS = "-debug" if WEBSERVER_MODE == 'PROD': GEMMAOPTS = "-no-check" -def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf=0.01): +def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf=0.01, first_run=True, gwa_output_filename=None): """Generates p-values for each marker using GEMMA""" if this_dataset.group.genofile != None: @@ -20,127 +20,114 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf else: genofile_name = this_dataset.group.name - trait_filename = str(this_trait.name) + "_" + str(this_dataset.name) + "_pheno" - gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename) - - if not os.path.isfile("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)): - open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name), "w+") - - this_chromosomes = this_dataset.species.chromosomes.chromosomes - chr_list_string = "" - for i in range(len(this_chromosomes)): - if i < (len(this_chromosomes) - 1): - chr_list_string += this_chromosomes[i+1].name + "," - else: - chr_list_string += this_chromosomes[i+1].name - - if covariates != "": - gen_covariates_file(this_dataset, covariates) - - k_output_filename = this_dataset.group.name + "_K_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) - gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) - if use_loco == "True": - generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename) - logger.debug("k_command:" + generate_k_command) - os.system(generate_k_command) - - gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename) - if covariates != "": - gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'), - this_dataset.group.name, - flat_files('genotype/bimbam'), - genofile_name, - maf, - TEMPDIR, - gwa_output_filename) - else: - gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), - genofile_name, - maf, - TEMPDIR, - gwa_output_filename) - - else: - generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename) - #generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # trait_filename, - # flat_files('genotype/bimbam'), - # genofile_name, - # TEMPDIR, - # k_output_filename) - - logger.debug("k_command:" + generate_k_command) - os.system(generate_k_command) - - gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - trait_filename, - flat_files('genotype/bimbam'), - genofile_name, - TEMPDIR, - k_output_filename, - maf) - - #gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (flat_files('genotype/bimbam'), - # genofile_name, - # flat_files('genotype/bimbam'), - # genofile_name) - - - if covariates != "": - gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), - this_dataset.group.name, - webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) - else: - gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, - genofile_name) - - #if covariates != "": - # gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'), - # this_dataset.group.name, - # flat_files('genotype/bimbam'), - # genofile_name, - # maf, - # TEMPDIR, - # gwa_output_filename) - #else: - # gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), - # genofile_name, - # maf, - # TEMPDIR, - # gwa_output_filename) - - logger.debug("gemma_command:" + gemma_command) - os.system(gemma_command) + if first_run: + trait_filename = str(this_trait.name) + "_" + str(this_dataset.name) + "_pheno" + gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename) + + if not os.path.isfile("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)): + open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name), "w+") + + k_output_filename = this_dataset.group.name + "_K_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + + this_chromosomes = this_dataset.species.chromosomes.chromosomes + chr_list_string = "" + for i in range(len(this_chromosomes)): + if i < (len(this_chromosomes) - 1): + chr_list_string += this_chromosomes[i+1].name + "," + else: + chr_list_string += this_chromosomes[i+1].name + + if covariates != "": + gen_covariates_file(this_dataset, covariates) + + if use_loco == "True": + generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename, + flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + k_output_filename) + logger.debug("k_command:" + generate_k_command) + os.system(generate_k_command) + + gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename) + if covariates != "": + gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + genofile_name, + maf, + TEMPDIR, + gwa_output_filename) + else: + gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), + genofile_name, + maf, + TEMPDIR, + gwa_output_filename) + + else: + generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename, + flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + k_output_filename) + #generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), + # genofile_name, + # flat_files('genotype/bimbam'), + # trait_filename, + # flat_files('genotype/bimbam'), + # genofile_name, + # TEMPDIR, + # k_output_filename) + + logger.debug("k_command:" + generate_k_command) + os.system(generate_k_command) + + gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + trait_filename, + flat_files('genotype/bimbam'), + genofile_name, + TEMPDIR, + k_output_filename, + maf) + + #gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (flat_files('genotype/bimbam'), + # genofile_name, + # flat_files('genotype/bimbam'), + # genofile_name) + + + if covariates != "": + gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'), + this_dataset.group.name, + webqtlConfig.GENERATED_IMAGE_DIR, + genofile_name) + else: + gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR, + genofile_name) + + + logger.debug("gemma_command:" + gemma_command) + os.system(gemma_command) if use_loco == "True": marker_obs = parse_loco_output(this_dataset, gwa_output_filename) + return marker_obs, gwa_output_filename else: - #marker_obs = parse_loco_output(this_dataset, gwa_output_filename) marker_obs = parse_gemma_output(genofile_name) - - return marker_obs + return marker_obs def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename): """Generates phenotype file for GEMMA""" diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index c0d6dc0b..a0466c0f 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -175,10 +175,19 @@ class RunMapping(object): self.dataset.group.genofile = self.genofile_string.split(":")[0] self.dataset.group.get_markers() if self.mapping_method == "gemma": + self.first_run = True + self.gwa_filename = None + if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc) + self.first_run = False + if 'gwa_filename' in start_vars: + self.gwa_filename = start_vars['gwa_filename'] self.score_type = "-log(p)" self.manhattan_plot = True with Bench("Running GEMMA"): - marker_obs = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf) + if self.use_loco == "True": + marker_obs, self.gwa_filename = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.gwa_filename) + else: + marker_obs = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py index ea7ab1b9..1ca5ecff 100644 --- a/wqflask/wqflask/parser.py +++ b/wqflask/wqflask/parser.py @@ -33,20 +33,18 @@ def parse(pstring): """ pstring = re.split(r"""(?:(\w+\s*=\s*[\('"\[][^)'"]*[\)\]'"]) | # LRS=(1 2 3), cisLRS=[4 5 6], etc (\w+\s*[=:\>\<][\w\*]+) | # wiki=bar, GO:foobar, etc + (".*?") | ('.*?') | # terms in quotes, i.e. "brain weight" ([\w\*]+)) # shh, brain, etc """, pstring, flags=re.VERBOSE) + pstring = [item.strip() for item in pstring if item and item.strip()] - print(pstring) + logger.debug("pstring:", pstring) items = [] separators = [re.escape(x) for x in ("<=", ">=", ":", "=", "<", ">")] separators = '(%s)' % ("|".join(separators)) - logger.debug("separators:", separators) - - - for item in pstring: splat = re.split(separators, item) logger.debug("splat is:", splat) @@ -70,6 +68,8 @@ def parse(pstring): separator=separator, search_term=value) else: + if (item[0] == "\"" and item[-1] == "\"") or (item[0] == "'" and item[-1] == "'"): + item = item[1:-1] term = dict(key=None, separator=None, search_term=[item]) 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 28af232d..95d3a537 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -267,6 +267,14 @@ } }); + $("li.mapping_tab").click(function() { + if ($(this).hasClass("rqtl")){ + $(".rqtl_description").css("display", "block"); + } else { + $(".rqtl_description").css("display", "none"); + } + }); + toggle_enable_disable = function(elem) { return $(elem).prop("disabled", !$(elem).prop("disabled")); }; diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 72d9d0dd..317747c1 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -16,6 +16,10 @@ <input type="hidden" name="dataset" value="{{ dataset.name }}"> <input type="hidden" name="genofile" value="{{ genofile_string }}"> <input type="hidden" name="geno_db_exists" value="{{ geno_db_exists }}"> + <input type="hidden" name="first_run" value="{{ first_run }}"> + {% if gwa_filename is defined %} + <input type="hidden" name="gwa_filename" value="{{ gwa_filename }}"> + {% endif %} <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> {% for sample in samples %} diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index b5ed1c8f..b5c37b8b 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -5,23 +5,23 @@ <ul class="nav nav-pills"> {% if dataset.group.mapping_id == "1" %} - <li class="active"> + <li class="mapping_tab active"> <a href="#gemma" data-toggle="tab">GEMMA</a> </li> - <li> + <li class="mapping_tab"> <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> </li> - <li> + <li class="mapping_tab rqtl"> <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> </li> {% endif %} {% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %} - <li class="active"> + <li class="mapping_tab active"> <a href="#gemma_plink" data-toggle="tab">GEMMA</a> </li> {% elif mapping_method == "PLINK" %} - <li> + <li class="mapping_tab"> <a href="#plink" data-toggle="tab">PLINK</a> </li> {% endif %} @@ -353,6 +353,9 @@ <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd> {% endif %} </dl> + <div class="rqtl_description" style="padding-top: 40px; display: none;"> + More information on R/qtl mapping models and methods can be found <a href="http://www.rqtl.org/tutorials/rqtltour.pdf">here</a>. + </div> </div> <div id="mapping_result_holder_wrapper" style="display:none;"> <div id="mapping_result_holder"></div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index d00f067e..bff3aa2a 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -575,6 +575,8 @@ def mapping_results_page(): 'group', 'species', 'vals', + 'first_run', + 'gwa_filename', 'geno_db_exists', 'method', 'mapping_results_path', |