From 10b8dc7af35f0d221daf121d0e3c0a52d9223368 Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Wed, 29 Apr 2020 04:38:42 -0500
Subject: Fixing loading of the ITP data as a 4way cross, worked on
 http://gn2-test3.genenetwork.org/

---
 wqflask/wqflask/marker_regression/rqtl_mapping.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index e1aa290b..9909b6d4 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')
@@ -139,7 +139,11 @@ 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 == '4-way'){
+           cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE)                 # Load the created cross file using R/qtl read.cross
+         }else{
+           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)
       }
-- 
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