diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 9 |
1 files changed, 7 insertions, 2 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index f593ae91..c70fbbec 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -10,6 +10,7 @@ from base.trait import create_trait from base.data_set import create_dataset from utility import webqtlUtil from utility.tools import locate, TEMPDIR +from wqflask.marker_regression.gemma_mapping import generate_random_n_string from flask import g import utility.logger @@ -148,13 +149,17 @@ def generate_cross_from_rdata(dataset): """ % (rdata_location)) def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly + + cross_filename = (f"{str(dataset.group.name)}_" + f"{generate_random_n_string(6)}") + 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){ + GENOtoCSVR <- function(genotypes = '%s', out = '%s.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 type <- getGenoCode(header, 'type') @@ -188,7 +193,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur } return(cross) } - """ % (dataset.group.genofile, scale_units)) + """ % (dataset.group.genofile, cross_filename, scale_units)) def add_perm_strata(cross, perm_strata): col_string = 'c("the_strata")' |