aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--etc/default_settings.py1
-rw-r--r--wqflask/base/data_set.py4
-rw-r--r--wqflask/utility/tools.py4
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py1
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py17
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json51
-rw-r--r--wqflask/wqflask/templates/docs.html4
7 files changed, 53 insertions, 29 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py
index a1fe81e5..a16ac3ad 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -91,4 +91,5 @@ JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript"
# ---- GN2 Executables (overwrite for testing only)
# PLINK_COMMAND = str.strip(os.popen("which plink2").read())
# GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
+REAPER_COMMAND = HOME + "/gn2-zach/rust-qtlreaper/target/release/qtlreaper"
# GEMMA_WRAPPER_COMMAND = str.strip(os.popen("which gemma-wrapper").read())
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d766e284..41de8492 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -46,6 +46,8 @@ from utility import chunks
from utility import gen_geno_ob
from utility.tools import locate, locate_ignore_error, flat_files
+from wqflask.api import gen_menu
+
from maintenance import get_group_samplelists
from MySQLdb import escape_string as escape
@@ -92,7 +94,7 @@ Publish or ProbeSet. E.g.
"""
self.datasets = {}
if USE_GN_SERVER:
- data = menu_main()
+ data = gen_menu.gen_dropdown_json()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
with open(file_name, 'r') as fh:
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 8b2260f5..31ab2046 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -107,6 +107,9 @@ def js_path(module=None):
return try_guix
raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
+def reaper_command(guess=None):
+ return get_setting("REAPER_COMMAND",guess)
+
def gemma_command(guess=None):
return assert_bin(get_setting("GEMMA_COMMAND",guess))
@@ -274,6 +277,7 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT')
SMTP_USERNAME = get_setting('SMTP_USERNAME')
SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
+REAPER_COMMAND = app_set("REAPER_COMMAND",reaper_command())
GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
assert(GEMMA_COMMAND is not None)
PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3bcd613f..d9601405 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1790,7 +1790,6 @@ class DisplayMappingResults(object):
m = 0
thisLRSColor = self.colorCollection[0]
if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
-
if self.manhattan_plot != True:
canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 2bde2b53..6e9fe85c 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -36,7 +36,7 @@ from utility import helper_functions
from utility import Plot, Bunch
from utility import temp_data
from utility.benchmark import Bench
-from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
+from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping, rust_reaper_mapping
from utility.tools import locate, locate_ignore_error, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
from utility.external import shell
@@ -242,7 +242,8 @@ class RunMapping(object):
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
logger.info("Running qtlreaper")
- results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
+
+ results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = rust_reaper_mapping.run_reaper(self.this_trait,
self.dataset,
self.samples,
self.vals,
@@ -253,6 +254,18 @@ class RunMapping(object):
self.do_control,
self.control_marker,
self.manhattan_plot)
+
+ # results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
+ # self.dataset,
+ # self.samples,
+ # self.vals,
+ # self.json_data,
+ # self.num_perm,
+ # self.bootCheck,
+ # self.num_bootstrap,
+ # self.do_control,
+ # self.control_marker,
+ # self.manhattan_plot)
elif self.mapping_method == "plink":
self.score_type = "-log(p)"
self.manhattan_plot = True
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 0d73213d..6531f5a0 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1440,7 +1440,7 @@
[
"None",
"HSBPublish",
- "HSB Phenotypes"
+ "HSB Published Phenotypes"
]
],
"Posterior Inferior Parietal Cortex mRNA": [
@@ -1721,7 +1721,7 @@
[
"None",
"B6D2Publish",
- "B6D2 Phenotypes"
+ "UTHSC-Glaucoma-Aged-Retina Phenotypes"
]
]
},
@@ -2248,6 +2248,11 @@
"Eye M430v2 WT Gpnmb (Sep08) RMA"
],
[
+ "382",
+ "Eye_M2_0908_WTWT",
+ "Eye M430v2 WT WT (Sep08) RMA"
+ ],
+ [
"279",
"Eye_M2_0908_R_WT",
"Eye M430v2 WT Tyrp1 (Sep08) RMA"
@@ -2258,11 +2263,6 @@
"Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
],
[
- "382",
- "Eye_M2_0908_WTWT",
- "Eye M430v2 WT WT (Sep08) RMA"
- ],
- [
"400",
"DBA2J-ONH-1212",
"Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
@@ -2500,6 +2500,11 @@
"245",
"UT_ILM_BXD_hipp_RSE_0909",
"UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv"
+ ],
+ [
+ "711",
+ "UTHSC_BXD_AgeHipp0515",
+ "UTHSC BXD Aged Hippocampus Affy MoGene1.0 ST (May15) RMA Gene Level"
]
],
"Hypothalamus mRNA": [
@@ -3029,16 +3034,6 @@
],
"Striatum mRNA": [
[
- "376",
- "DevStriatum_ILM6.2P3RInv_1111",
- "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv"
- ],
- [
- "377",
- "DevStriatum_ILM6.2P14RInv_1111",
- "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv"
- ],
- [
"399",
"Striatum_Exon_1212",
"HQF Striatum Affy Mouse Exon 1.0ST Gene Level (Dec09) RMA"
@@ -3049,6 +3044,16 @@
"HQF Striatum Affy Mouse Exon 1.0ST Exon Level (Dec09) RMA"
],
[
+ "376",
+ "DevStriatum_ILM6.2P3RInv_1111",
+ "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv"
+ ],
+ [
+ "377",
+ "DevStriatum_ILM6.2P14RInv_1111",
+ "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv"
+ ],
+ [
"285",
"UTHSC_Striatum_RankInv_1210",
"HQF BXD Striatum ILM6.1 (Dec10v2) RankInv"
@@ -3555,6 +3560,11 @@
],
"Hippocampus mRNA": [
[
+ "211",
+ "Illum_LXS_Hipp_RSS_1008",
+ "Hippocampus Illumina RSS (Oct08) RankInv beta"
+ ],
+ [
"213",
"Illum_LXS_Hipp_NOS_1008",
"Hippocampus Illumina NOS (Oct08) RankInv beta"
@@ -3575,11 +3585,6 @@
"Hippocampus Illumina NOE (Oct08) RankInv beta"
],
[
- "211",
- "Illum_LXS_Hipp_RSS_1008",
- "Hippocampus Illumina RSS (Oct08) RankInv beta"
- ],
- [
"143",
"Illum_LXS_Hipp_loess0807",
"Hippocampus Illumina (Aug07) LOESS"
@@ -3835,7 +3840,7 @@
[
"None",
"HSNIH-RGSMCPublish",
- "HSNIH-RGSMC Phenotypes"
+ "HSNIH Published Phenotypes"
]
]
},
diff --git a/wqflask/wqflask/templates/docs.html b/wqflask/wqflask/templates/docs.html
index c485f757..1a241ce7 100644
--- a/wqflask/wqflask/templates/docs.html
+++ b/wqflask/wqflask/templates/docs.html
@@ -6,9 +6,9 @@
<div class="container">
<h3>{{title}}</h3>
<div style="text-align: right;">
- <a href="docedit?entry={{entry}}">
+ <!--<a href="docedit?entry={{entry}}">-->
<img style="width: 16px;" src="/static/new/images/edit.gif">
- </a>
+ <!--</a>-->
</div>
{{content|safe}}
</div>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 15:55:21 +0000