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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py6
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py221
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py11
-rw-r--r--wqflask/wqflask/parser.py10
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js8
-rw-r--r--wqflask/wqflask/templates/mapping_results.html4
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html13
-rw-r--r--wqflask/wqflask/views.py2
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',
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 07:07:43 +0000