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-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py7
1 files changed, 6 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 9909b6d4..c1a56787 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -140,11 +140,16 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(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') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ 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))