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authorzsloan2020-04-29 11:17:23 -0500
committerGitHub2020-04-29 11:17:23 -0500
commitcd05cb4782c22abdf299f033a39ccfa82be38596 (patch)
treeb686af7171728db2a943085fcb23250a04f04777
parent86d885f5f2e1069a5b1606296a71992805486aec (diff)
parent98d54f1861f2bbc82cffa049fef408b43351688a (diff)
downloadgenenetwork2-cd05cb4782c22abdf299f033a39ccfa82be38596.tar.gz
Merge pull request #385 from DannyArends/testing
Fixing loading of the ITP data as a 4way cross
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py15
1 files changed, 12 insertions, 3 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index e1aa290b..c1a56787 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -128,7 +128,7 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
if(type == '4-way'){
genocodes <- c('1','2','3','4')
} else {
- genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
}
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')
@@ -139,8 +139,17 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
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
+ if(type == '4-way'){
+ cat('Loading in as 4-WAY\n')
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ }else{
+ cat('Loading in as normal\n')
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ }
+ if(type == 'riset'){
+ cat('Converting to RISELF\n')
+ cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ }
return(cross)
}
""" % (dataset.group.genofile))