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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py46
1 files changed, 29 insertions, 17 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 60bc721e..9a3ff073 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -76,7 +76,10 @@ 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']
print("DOING RQTL GENO")
@@ -232,18 +235,21 @@ 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 +257,9 @@ 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
}
""")
@@ -263,6 +271,7 @@ 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
@@ -285,25 +294,24 @@ 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)
+ covar = self.create_covariates(cross_object)
+ if(r_sum(covar)[0] > 0):
+ print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar)
else:
- result_data_frame = scanone(cross_object, pheno = "the_pheno")
+ 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(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 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))
+ 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)
@@ -318,7 +326,11 @@ 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"]