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authorzsloan2016-02-15 18:00:18 +0000
committerzsloan2016-02-15 18:00:18 +0000
commit7f5536635ac20f7c670e4dc8e650f27d47503d78 (patch)
treebf82bd9ddbc2d38d4ac2f93a12ccf27dd1450ebc
parent67cf280f32ef0822b873f94f3dd103eb7101c737 (diff)
downloadgenenetwork2-7f5536635ac20f7c670e4dc8e650f27d47503d78.tar.gz
Fixed R/qtl mapping so the group (BXD, etc) isn't hardcoded
Removed an extraneous </td> tag from the show trait page
-rwxr-xr-xwqflask/other_config/nginx_conf/gn2-zach.conf (renamed from wqflask/other_config/nginx_conf/gn2_zach.conf)2
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py7
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html4
-rwxr-xr-xwqflask/wqflask/templates/show_trait_statistics.html2
4 files changed, 7 insertions, 8 deletions
diff --git a/wqflask/other_config/nginx_conf/gn2_zach.conf b/wqflask/other_config/nginx_conf/gn2-zach.conf
index 1614bcb4..38347292 100755
--- a/wqflask/other_config/nginx_conf/gn2_zach.conf
+++ b/wqflask/other_config/nginx_conf/gn2-zach.conf
@@ -2,7 +2,7 @@ server {
# Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
listen 80;
- server_name gn2_zach.genenetwork.org;
+ server_name gn2-zach.genenetwork.org;
access_log /var/log/nginx/access.log;
error_log /var/log/nginx/error.log;
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d3ee344d..c16c885e 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -298,6 +298,9 @@ class MarkerRegression(object):
def geno_to_rqtl_function(self): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
print("Adding some custom helper functions to the R environment")
+
+
+
ro.r("""
trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
@@ -306,7 +309,7 @@ class MarkerRegression(object):
return(trim(strsplit(header[mat],':')[[1]][2]))
}
- GENOtoCSVR <- function(genotypes = 'BXD.geno', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
+ GENOtoCSVR <- function(genotypes = '%s', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
header = readLines(genotypes, 40) # Assume a geno header is not longer than 40 lines
toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers
@@ -325,7 +328,7 @@ class MarkerRegression(object):
if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
return(cross)
}
- """)
+ """ % (self.dataset.group.name + ".geno"))
def run_rqtl_geno(self):
print("Calling R/qtl")
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index b4f5b6c2..29239adb 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -189,8 +189,6 @@
}
});
- console.time("Creating table");
-
$('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'yellow')
{% if sample_groups[0].se_exists() %}
$('#samples_primary, #samples_other').DataTable( {
@@ -218,10 +216,8 @@
},
"paging": false
} );
- console.timeEnd("Creating table");
{% else %}
- console.time("Creating table");
$('#samples_primary, #samples_other').DataTable( {
"columns": [
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 34fa2216..2183dd30 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -110,7 +110,7 @@
<div>
More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
- about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
+ about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a>
</div>
</div>