From 18cf0075003b70b2d97f9fe20794b8ed3f6e1233 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 15 Sep 2016 17:10:51 +0000
Subject: Conflict in wqflask/wqflask/templates/show_trait_mapping_tools.html

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 3d9c2521..9c1101ca 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -32,6 +32,18 @@
                 {% if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" %}
                 <div class="tab-pane active" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
+                        {% if genofiles and genofiles|length>0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="genofiles" class="col-xs-3 control-label">Geno&nbsp;File</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                                <select name="genofile" class="form-control">
+                                    {% for item in genofiles %}
+                                    <option value="{{item[0]}}">{{item[1]}}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
+                        {% endif %}
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
@@ -90,8 +102,8 @@
 
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Marker Regr.</label>
-                            <div class="col-xs-12 controls">                      
+                            <label style="text-align:left;" class="col-xs-3 control-label">Marker<br>Regression</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">                      
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_reaper" value="True">
                                     Yes
-- 
cgit v1.2.3


From 5fd49a1e036b02eaa82bdb8ce747a3c2cbc8c8de Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 3 Oct 2016 16:46:47 +0000
Subject: Moved rqtl mapping code out of marker_regression and into its own
 file.

Later we will want to run all mapping methods outside of the web server, though
---
 .../wqflask/marker_regression/marker_regression.py | 191 +--------------------
 wqflask/wqflask/marker_regression/rqtl_mapping.py  | 190 ++++++++++++++++++++
 2 files changed, 192 insertions(+), 189 deletions(-)
 create mode 100644 wqflask/wqflask/marker_regression/rqtl_mapping.py

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d2b27991..bb964961 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -35,7 +35,7 @@ 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
+from wqflask.marker_regression import gemma_mapping, rqtl_mapping
 
 from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
 from utility.external import shell
@@ -166,7 +166,7 @@ class MarkerRegression(object):
             self.model = start_vars['mapmodel_rqtl_geno']
             if start_vars['pair_scan'] == "true":
                 self.pair_scan = True
-            results = self.run_rqtl_geno()
+            results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
         elif self.mapping_method == "reaper":
             if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
                 if "additiveCheck" in start_vars:
@@ -349,193 +349,6 @@ class MarkerRegression(object):
 
         count, p_values = self.parse_rqtl_output(plink_output_filename)
 
-    def geno_to_rqtl_function(self):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
-
-        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(trim(strsplit(header[mat],':')[[1]][2]))
-           }
-
-           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
-
-             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), 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
-                              c('sex', '', '', sex),                                                                           # Sex phenotype for the mice
-                              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)
-             cross = read.cross(file=out, 'csvr', genotypes=genocodes)                                                         # Load the created cross file using R/qtl read.cross
-             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):
-        self.geno_to_rqtl_function()
-
-        ## 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 sum function
-        plot          = ro.r["plot"]                    # Map the plot function
-        postscript    = ro.r["postscript"]              # Map the postscript function
-        png           = ro.r["png"]                     # Map the png function
-        dev_off       = ro.r["dev.off"]                 # Map the device off 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
-        GENOtoCSVR      = ro.r["GENOtoCSVR"]            # Map the local GENOtoCSVR function
-
-        crossname = self.dataset.group.name
-        genofilelocation  = locate(crossname + ".geno", "genotype")
-        crossfilelocation = TMPDIR + crossname + ".cross"
-
-        #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation)
-
-        cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)                                  # TODO: Add the SEX if that is available
-
-        if self.manhattan_plot:
-            cross_object = calc_genoprob(cross_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
-
-        # for debug: write_cross(cross_object, "csvr", "test.csvr")
-
-        # Scan for QTLs
-        covar = self.create_covariates(cross_object)                                                    # Create the additive covariate matrix
-
-        if self.pair_scan:
-            if self.do_control == "true":                                                # If sum(covar) > 0 we have a covariate matrix
-                print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=self.model, method=self.method, n_cluster = 16)
-            else:
-                print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=self.model, method=self.method, n_cluster = 16)
-
-            #print("Pair scan results:", result_data_frame)
-
-            self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
-            png(file=TEMPDIR+self.pair_scan_filename)
-            plot(result_data_frame)
-            dev_off()
-
-            return self.process_pair_scan_results(result_data_frame)
-
-        else:
-            if self.do_control == "true":
-                print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=self.model, method=self.method)
-            else:
-                print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=self.model, method=self.method)
-
-            if self.num_perm > 0 and self.permCheck == "ON":                                                                   # Do permutation (if requested by user)
-                if self.do_control == "true":
-                    perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = self.num_perm, model=self.model, method=self.method)
-                else:
-                    perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = self.num_perm, model=self.model, method=self.method)
-
-                self.process_rqtl_perm_results(perm_data_frame)                                          # Functions that sets the thresholds for the webinterface
-
-            return self.process_rqtl_results(result_data_frame)
-
-    def add_phenotype(self, cross, pheno_as_string):
-        ro.globalenv["the_cross"] = cross
-        ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), the_pheno = '+ pheno_as_string +')')
-        return ro.r["the_cross"]
-
-    def create_covariates(self, cross):
-        ro.globalenv["the_cross"] = cross
-        ro.r('genotypes <- pull.geno(the_cross)')                             # Get the genotype matrix
-        userinputS = self.control_marker.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('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"]
-
-    def sanitize_rqtl_phenotype(self):
-        pheno_as_string = "c("
-        for i, val in enumerate(self.vals):
-            if val == "x":
-                if i < (len(self.vals) - 1):
-                    pheno_as_string +=  "NA,"
-                else:
-                    pheno_as_string += "NA"
-            else:
-                if i < (len(self.vals) - 1):
-                    pheno_as_string += str(val) + ","
-                else:
-                    pheno_as_string += str(val)
-        pheno_as_string += ")"
-        return pheno_as_string
-
-    def process_pair_scan_results(self, result):
-        pair_scan_results = []
-
-        result = result[1]
-        output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-        #print("R/qtl scantwo output:", output)
-
-        for i, line in enumerate(result.iter_row()):
-            marker = {}
-            marker['name'] = result.rownames[i]
-            marker['chr1'] = output[i][0]
-            marker['Mb'] = output[i][1]
-            marker['chr2'] = int(output[i][2])
-            pair_scan_results.append(marker)
-
-        #print("pair_scan_results:", pair_scan_results)
-
-        return pair_scan_results
-
-    def process_rqtl_results(self, result):        # TODO: how to make this a one liner and not copy the stuff in a loop
-        qtl_results = []
-
-        output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-        #print("R/qtl scanone output:", output)
-
-        for i, line in enumerate(result.iter_row()):
-            marker = {}
-            marker['name'] = result.rownames[i]
-            marker['chr'] = output[i][0]
-            marker['Mb'] = output[i][1]
-            marker['lod_score'] = output[i][2]
-            qtl_results.append(marker)
-
-        return qtl_results
-
-    def process_rqtl_perm_results(self, results):
-        perm_vals = []
-        for line in str(results).split("\n")[1:(self.num_perm+1)]:
-            #print("R/qtl permutation line:", line.split())
-            perm_vals.append(float(line.split()[1]))
-
-        self.perm_output = perm_vals
-        self.suggestive = np.percentile(np.array(perm_vals), 67)
-        self.significant = np.percentile(np.array(perm_vals), 95)
-
-        return self.suggestive, self.significant
-
-
     def run_plink(self):
         plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
 
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
new file mode 100644
index 00000000..53ea6053
--- /dev/null
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -0,0 +1,190 @@
+import rpy2.robjects as ro
+
+from base.webqtlConfig import TMPDIR
+from utility import webqtlUtil
+from utility.tools import locate, TEMPDIR
+
+def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control, control_marker, manhattan_plot, pair_scan):
+    geno_to_rqtl_function(dataset)
+
+    ## 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 sum function
+    plot          = ro.r["plot"]                    # Map the plot function
+    postscript    = ro.r["postscript"]              # Map the postscript function
+    png           = ro.r["png"]                     # Map the png function
+    dev_off       = ro.r["dev.off"]                 # Map the device off 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
+    GENOtoCSVR      = ro.r["GENOtoCSVR"]            # Map the local GENOtoCSVR function
+
+    crossname = dataset.group.name
+    genofilelocation  = locate(crossname + ".geno", "genotype")
+    crossfilelocation = TMPDIR + crossname + ".cross"
+
+    #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation)
+
+    cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)                                  # TODO: Add the SEX if that is available
+
+    if manhattan_plot:
+        cross_object = calc_genoprob(cross_object)
+    else:
+        cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
+
+    cross_object = add_phenotype(cross_object, sanitize_rqtl_phenotype(vals))                 # Add the phenotype
+
+    # for debug: write_cross(cross_object, "csvr", "test.csvr")
+
+    # Scan for QTLs
+    covar = create_covariates(control_marker, cross_object)                                                    # Create the additive covariate matrix
+
+    if pair_scan:
+        if do_control == "true":                                                # If sum(covar) > 0 we have a covariate matrix
+            print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method, n_cluster = 16)
+        else:
+            print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
+
+        #print("Pair scan results:", result_data_frame)
+
+        pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
+        png(file=TEMPDIR+pair_scan_filename)
+        plot(result_data_frame)
+        dev_off()
+
+        return process_pair_scan_results(result_data_frame)
+    else:
+        if do_control == "true":
+            print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method)
+        else:
+            print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
+
+        if num_perm > 0 and permCheck == "ON":                                                                   # Do permutation (if requested by user)
+            if do_control == "true":
+                perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = num_perm, model=model, method=method)
+            else:
+                perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
+
+            process_rqtl_perm_results(num_perm, perm_data_frame)                                          # Functions that sets the thresholds for the webinterface
+
+        return process_rqtl_results(result_data_frame)
+
+def geno_to_rqtl_function(dataset):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+
+    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(trim(strsplit(header[mat],':')[[1]][2]))
+       }
+
+       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
+
+         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), 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
+                          c('sex', '', '', sex),                                                                           # Sex phenotype for the mice
+                          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)
+         cross = read.cross(file=out, 'csvr', genotypes=genocodes)                                                         # Load the created cross file using R/qtl read.cross
+         if(type == 'riset') cross <- convert2riself(cross)                                                                # If its a RIL, convert to a RIL in R/qtl
+         return(cross)
+      }
+    """ % (dataset.group.name + ".geno"))
+        
+def add_phenotype(cross, pheno_as_string):
+    ro.globalenv["the_cross"] = cross
+    ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), the_pheno = '+ pheno_as_string +')')
+    return ro.r["the_cross"]
+
+def create_covariates(control_marker, cross):
+    ro.globalenv["the_cross"] = cross
+    ro.r('genotypes <- pull.geno(the_cross)')                             # Get the genotype matrix
+    userinputS = control_marker.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('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"]
+
+def sanitize_rqtl_phenotype(vals):
+    pheno_as_string = "c("
+    for i, val in enumerate(vals):
+        if val == "x":
+            if i < (len(vals) - 1):
+                pheno_as_string +=  "NA,"
+            else:
+                pheno_as_string += "NA"
+        else:
+            if i < (len(vals) - 1):
+                pheno_as_string += str(val) + ","
+            else:
+                pheno_as_string += str(val)
+    pheno_as_string += ")"
+    return pheno_as_string
+
+def process_pair_scan_results(result):
+    pair_scan_results = []
+
+    result = result[1]
+    output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+    #print("R/qtl scantwo output:", output)
+
+    for i, line in enumerate(result.iter_row()):
+        marker = {}
+        marker['name'] = result.rownames[i]
+        marker['chr1'] = output[i][0]
+        marker['Mb'] = output[i][1]
+        marker['chr2'] = int(output[i][2])
+        pair_scan_results.append(marker)
+
+    #print("pair_scan_results:", pair_scan_results)
+
+    return pair_scan_results
+
+def process_rqtl_results(result):        # TODO: how to make this a one liner and not copy the stuff in a loop
+    qtl_results = []
+
+    output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+    #print("R/qtl scanone output:", output)
+
+    for i, line in enumerate(result.iter_row()):
+        marker = {}
+        marker['name'] = result.rownames[i]
+        marker['chr'] = output[i][0]
+        marker['Mb'] = output[i][1]
+        marker['lod_score'] = output[i][2]
+        qtl_results.append(marker)
+
+    return qtl_results
+
+def process_rqtl_perm_results(num_perm, results):
+    perm_vals = []
+    for line in str(results).split("\n")[1:(num_perm+1)]:
+        #print("R/qtl permutation line:", line.split())
+        perm_vals.append(float(line.split()[1]))
+
+    perm_output = perm_vals
+    suggestive = np.percentile(np.array(perm_vals), 67)
+    significant = np.percentile(np.array(perm_vals), 95)
+
+    return perm_output, suggestive, significant 
\ No newline at end of file
-- 
cgit v1.2.3


From 6a0a3626baad96deb1e8dc7d27fe1fa15e8c5b98 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 3 Oct 2016 19:16:56 +0000
Subject: Fixed problem that caused R/qtl with permutations to not work
 correctly

---
 .../wqflask/marker_regression/marker_regression.py |  5 +++-
 wqflask/wqflask/marker_regression/rqtl_mapping.py  | 35 ++++++++++++----------
 2 files changed, 23 insertions(+), 17 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index bb964961..f2a2eb8c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -166,7 +166,10 @@ class MarkerRegression(object):
             self.model = start_vars['mapmodel_rqtl_geno']
             if start_vars['pair_scan'] == "true":
                 self.pair_scan = True
-            results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
+            if self.permCheck and self.num_perm > 0:
+                perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
+            else:
+                results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
         elif self.mapping_method == "reaper":
             if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
                 if "additiveCheck" in start_vars:
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 53ea6053..93bf717c 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -1,4 +1,5 @@
 import rpy2.robjects as ro
+import numpy as np
 
 from base.webqtlConfig import TMPDIR
 from utility import webqtlUtil
@@ -72,9 +73,10 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
             else:
                 perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
 
-            process_rqtl_perm_results(num_perm, perm_data_frame)                                          # Functions that sets the thresholds for the webinterface
-
-        return process_rqtl_results(result_data_frame)
+            perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame)          # Functions that sets the thresholds for the webinterface
+            return perm_output, suggestive, significant, process_rqtl_results(result_data_frame)
+        else:
+            return process_rqtl_results(result_data_frame)
 
 def geno_to_rqtl_function(dataset):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
 
@@ -161,6 +163,19 @@ def process_pair_scan_results(result):
 
     return pair_scan_results
 
+def process_rqtl_perm_results(num_perm, results):
+    perm_vals = []
+    for line in str(results).split("\n")[1:(num_perm+1)]:
+        #print("R/qtl permutation line:", line.split())
+        perm_vals.append(float(line.split()[1]))
+
+    perm_output = perm_vals
+    suggestive = np.percentile(np.array(perm_vals), 67)
+    significant = np.percentile(np.array(perm_vals), 95)
+    print("SIGNIFICANT:", significant)
+
+    return perm_output, suggestive, significant
+    
 def process_rqtl_results(result):        # TODO: how to make this a one liner and not copy the stuff in a loop
     qtl_results = []
 
@@ -175,16 +190,4 @@ def process_rqtl_results(result):        # TODO: how to make this a one liner an
         marker['lod_score'] = output[i][2]
         qtl_results.append(marker)
 
-    return qtl_results
-
-def process_rqtl_perm_results(num_perm, results):
-    perm_vals = []
-    for line in str(results).split("\n")[1:(num_perm+1)]:
-        #print("R/qtl permutation line:", line.split())
-        perm_vals.append(float(line.split()[1]))
-
-    perm_output = perm_vals
-    suggestive = np.percentile(np.array(perm_vals), 67)
-    significant = np.percentile(np.array(perm_vals), 95)
-
-    return perm_output, suggestive, significant 
\ No newline at end of file
+    return qtl_results 
\ No newline at end of file
-- 
cgit v1.2.3


From da127da677a8976675fb95d75213dd3e5326fb36 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 4 Oct 2016 19:39:17 +0000
Subject: Fixed issue that caused adding to existing collections when not
 logged in to not work correctly.

The problem was that it would get the collection name from the "new_collection" field instead of the "existing_collections" dropdown.
---
 wqflask/wqflask/collect.py                     | 17 +++--------------
 wqflask/wqflask/templates/collections/add.html |  2 +-
 2 files changed, 4 insertions(+), 15 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 7e7aba89..81d03d6c 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -164,7 +164,7 @@ class UserCollection(object):
             if not uc:
                 return create_new("Default")
         else:
-            uc = model.UserCollection.query.get(params['existing_collection'])
+            uc = model.UserCollection.query.get(params['existing_collection'].split(":")[0])
         members =  list(uc.members_as_set()) #set(json.loads(uc.members))
         len_before = len(members)
 
@@ -218,7 +218,6 @@ def collections_add():
         anon_collections = user_manager.AnonUser().get_collections()
         collection_names = []
         for collection in anon_collections:
-            print("COLLECTION:", collection)
             collection_names.append({'id':collection['id'], 'name':collection['name']})
         return render_template("collections/add.html",
                                 traits = traits,
@@ -229,21 +228,17 @@ def collections_add():
 @app.route("/collections/new")
 def collections_new():
     params = request.args
-    #print("request.args in collections_new are:", params)
-
-    collection_name = params['new_collection']
     
-    if "anonymous_add" in params:
-        AnonCollection(name=collection_name).add_traits(params, "Default")
-        return redirect(url_for('view_collection'))
     if "sign_in" in params:
         return redirect(url_for('login'))
 
     if "create_new" in params:
         print("in create_new")
+        collection_name = params['new_collection']
         return create_new(collection_name)
     elif "add_to_existing" in params:
         print("in add to existing")
+        collection_name = params['existing_collection'].split(":")[1]
         if g.user_session.logged_in:
             return UserCollection().add_traits(params, collection_name)
         else:
@@ -251,7 +246,6 @@ def collections_new():
             ac.add_traits(params)
             return redirect(url_for('view_collection', collection_id=ac.id))
     else:
-        print("ELSE")
         CauseAnError
 
 
@@ -288,7 +282,6 @@ def create_new(collection_name):
         ac = AnonCollection(collection_name)
         ac.changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')       
         ac.add_traits(params)
-        print("Collection ID:", ac.id)
         return redirect(url_for('view_collection', collection_id=ac.id))
 
 @app.route("/collections/list")
@@ -367,7 +360,6 @@ def view_collection():
         uc_id = params['uc_id']
         uc = model.UserCollection.query.get(uc_id)
         traits = json.loads(uc.members)
-        print("traits are:", traits)
     else:
         user_collections = json.loads(Redis.get(user_manager.AnonUser().key))
         this_collection = {}
@@ -384,7 +376,6 @@ def view_collection():
     json_version = []
 
     for atrait in traits:
-        print("atrait is:", atrait)
         name, dataset_name = atrait.split(':')                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
         trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name)
@@ -393,8 +384,6 @@ def view_collection():
 
         json_version.append(trait_ob.jsonable())
 
-    print("trait_obs:", trait_obs)
-
     if "uc_id" in params:
         collection_info = dict(trait_obs=trait_obs,
                                uc = uc)
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 47b87d73..d45aa015 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -25,7 +25,7 @@
 
                 <select name="existing_collection" class="form-control">
                 {% for col in collections %}
-                    <option value="{{ col.id }}">{{ col.name }}</option>
+                    <option value="{{ col.id }}:{{ col.name }}">{{ col.name }}</option>
                 {% endfor %}
                 </select>
                 <br />
-- 
cgit v1.2.3