aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py69
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py5
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html83
-rwxr-xr-xwqflask/wqflask/views.py3
4 files changed, 104 insertions, 56 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 60bc721e..db92e14c 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -65,6 +65,7 @@ class MarkerRegression(object):
self.manhattan_plot = True
else:
self.manhattan_plot = False
+
self.maf = start_vars['maf'] # Minor allele frequency
self.suggestive = ""
self.significant = ""
@@ -76,9 +77,18 @@ class MarkerRegression(object):
elif self.mapping_method == "rqtl_plink":
qtl_results = self.run_rqtl_plink()
elif self.mapping_method == "rqtl_geno":
- self.num_perm = start_vars['num_perm']
+ if start_vars['num_perm'] == "":
+ self.num_perm = 0
+ else:
+ self.num_perm = start_vars['num_perm']
self.control = start_vars['control_marker']
+ if start_vars['pair_scan'] == "true":
+ self.pair_scan = True
+ else:
+ self.pair_scan = False
+ print("pair scan:", self.pair_scan)
+
print("DOING RQTL GENO")
qtl_results = self.run_rqtl_geno()
print("qtl_results:", qtl_results)
@@ -232,18 +242,21 @@ 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 a function to the R environment")
ro.r("""
+ trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
+
getGenoCode <- function(header, name = 'unk'){
mat = which(unlist(lapply(header,function(x){ length(grep(paste('@',name,sep=''), x)) })) == 1)
- return(strsplit(header[mat],'')[[1]][6])
+ return(trim(strsplit(header[mat],':')[[1]][2]))
}
GENOtoCSVR <- function(genotypes = 'BXD.geno', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
header = readLines(genotypes, 40)
toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers
+
genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
-
+ type <- getGenoCode(header, 'type')
genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
- cat('Genodata:', toskip, " ", dim(genodata), '\n')
+ cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
if(is.null(phenotype)) phenotype <- runif((ncol(genodata)-4)) # If there isn't a phenotype, generate a random one
if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4)) # If there isn't a sex phenotype, treat all as males
outCSVR <- rbind(c('Pheno', '', '', phenotype), # Phenotype
@@ -251,7 +264,9 @@ class MarkerRegression(object):
cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(qtl)
- return(read.cross(file=out, 'csvr', genotypes=genocodes)) # Load it using R/qtl read.cross
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes)
+ if(type == 'riset') cross <- convert2riself(cross)
+ return(cross) # Load it using R/qtl read.cross
}
""")
@@ -263,11 +278,13 @@ class MarkerRegression(object):
## Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
r_c = ro.r["c"] # Map the c function
+ r_sum = ro.r["sum"] # Map the ncol function
print(r_library("qtl")) # Load R/qtl
## Get pointers to some R/qtl functions
scanone = ro.r["scanone"] # Map the scanone function
+ scantwo = ro.r["scantwo"] # Map the scantwo function
calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
read_cross = ro.r["read.cross"] # Map the read.cross function
write_cross = ro.r["write.cross"] # Map the write.cross function
@@ -285,27 +302,37 @@ class MarkerRegression(object):
else:
cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
- cross_object = self.add_phenotype(cross_object, self.sanitize_rqtl_phenotype()) # Add the phenotype
+ cross_object = self.add_phenotype(cross_object, self.sanitize_rqtl_phenotype()) # Add the phenotype
# for debug: write_cross(cross_object, "csvr", "test.csvr")
# Scan for QTLs
- if(self.control.replace(" ", "") != ""):
- covar = self.create_covariates(cross_object)
- result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar)
- else:
- result_data_frame = scanone(cross_object, pheno = "the_pheno")
+ covar = self.create_covariates(cross_object)
- if int(self.num_perm) > 0: # Do permutation (if requested by user)
- if(self.control.replace(" ", "") != ""):
- covar = self.create_covariates(cross_object)
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm=int(self.num_perm))
+ if self.pair_scan:
+ if(r_sum(covar)[0] > 0):
+ print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar)
else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm=int(self.num_perm))
+ print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno")
+
+ print("pair scan results:", result_data_frame)
+
+ return 0
+ else:
+ if(r_sum(covar)[0] > 0):
+ print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar)
+ else:
+ print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno")
+
+ if int(self.num_perm) > 0: # Do permutation (if requested by user)
+ if(r_sum(covar)[0] > 0):
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm))
+ else:
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm))
- self.process_rqtl_perm_results(perm_data_frame) # Functions that sets the thresholds for the webinterface
+ self.process_rqtl_perm_results(perm_data_frame) # Functions that sets the thresholds for the webinterface
- return self.process_rqtl_results(result_data_frame)
+ return self.process_rqtl_results(result_data_frame)
def add_phenotype(self, cross, pheno_as_string):
ro.globalenv["the_cross"] = cross
@@ -318,7 +345,11 @@ class MarkerRegression(object):
userinputS = self.control.replace(" ", "").split(",") # TODO sanitize user input, Never Ever trust a user
covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
print("Marker names of selected covariates:", covariate_names)
- ro.r('covariates <- genotypes[,c(' + covariate_names + ')]') # Get the covariate matrix by using the marker name as index to the genotype file
+ ro.r('covnames <- c(' + covariate_names + ')')
+ ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
+ ro.r('covnames <- covnames[covInGeno]')
+ ro.r("cat('covnames (purged): ', covnames,'\n')")
+ ro.r('covariates <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
print("R/qtl matrix of covariates:", ro.r["covariates"])
return ro.r["covariates"]
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 62411640..11fd2644 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1310,6 +1310,9 @@ def get_nearest_marker(this_trait, this_db):
result = g.db.execute(query).fetchall()
print("result:", result)
- return result[0][0], result[1][0]
+ if result == []:
+ return "", ""
+ else:
+ return result[0][0], result[1][0]
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index d6c7b18e..946dab49 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -80,19 +80,31 @@
</div>
<div class="tab-pane" id="pylmm">
+
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
- <input name="num_perm_pylmm" value="0" type="text" class="form-control">
+ <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <input name="num_pylmm" value="2000" type="text" class="form-control">
</div>
</div>
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
</div>
<div class="mapping_method_fields form-group">
- <label class="col-xs-1 control-label">Manhattan Plot</label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
+ <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
+ <input name="control_pylmm" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
+ {% else %}
+ <input name="control_pylmm" value="" type="text" />
+ {% endif %}
+ </div>
+ </div>
+
+ <div class="mapping_method_fields form-group">
+ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+ <div class="col-xs-12 controls">
<label class="radio-inline">
<input type="radio" name="manhattan_plot_pylmm" value="true">
Yes
@@ -103,39 +115,30 @@
</label>
</div>
</div>
- <!--<div class="form-group" id="suggestive">
- <label for="suggestive_reaper" class="control-label" title="Control Locus">LOD score greater than: </label>
- <div class="controls">
- <input name="suggestive_reaper" type="text" value="0" class="form-control">
+ <div class="form-group">
+ <div style="padding-left:15px;" class="controls">
+ <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+ <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ </button>
</div>
- </div>-->
- </div>
-
- <div class="form-group">
- <label for="marker_regression_submit" class="col-xs-1 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
- Compute
- </button>
</div>
</div>
-
</div>
<div class="tab-pane" id="rqtl_geno">
<div style="padding: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
- <input name="num_perm_rqtl_geno" value="500" type="text" class="form-control">
+ <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
</div>
</div>
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
</div>
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-1 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-2 controls">
+ <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
<input name="control_rqtl_geno" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
{% else %}
@@ -144,8 +147,8 @@
</div>
</div>
<div class="mapping_method_fields form-group">
- <label class="col-xs-1 control-label">Manhattan&nbsp;Plot</label>
- <div style="margin-left:35px;" class="col-xs-4 controls">
+ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+ <div class="col-xs-12 controls">
<label class="radio-inline">
<input type="radio" name="manhattan_plot_rqtl" value="true">
Yes
@@ -156,17 +159,27 @@
</label>
</div>
</div>
- </div>
-
- <div class="form-group">
- <label for="marker_regression_submit" class="col-xs-1 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-4 controls">
- <button id="rqtl_geno_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
+ <div class="mapping_method_fields form-group">
+ <label style="text-align:left;" class="col-xs-12 control-label">Pair Scan</label>
+ <div class="col-xs-12 controls">
+ <label class="radio-inline">
+ <input type="radio" name="pair_scan" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="pair_scan" value="false" checked="">
+ No
+ </label>
+ </div>
+ </div>
+ <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">
+ <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ </button>
+ </div>
</div>
</div>
-
</div>
{% if dataset.group.species == 'human' %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 9110c5a1..e60852d5 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -285,7 +285,8 @@ def marker_regression_page():
'maf',
'manhattan_plot',
'control_marker',
- 'control_marker_db'
+ 'control_marker_db',
+ 'pair_scan'
)
start_vars = {}