Commit cd96b94a authored by Lucie  TROUBAT's avatar Lucie TROUBAT
Browse files

Pb2 with name outfolder

parent d0cb2588
......@@ -127,7 +127,7 @@ def generate_genome_matrices(region_files, reffolder, folder_output, prefix, suf
for reg in regions.iterrows():
# input reference panel file
fi_ref = "{0}/{1}{2}{3}".format(reffolder,prefix, reg[1]['chr'], suffix)
print(fi_ref)
#print(fi_ref)
chr_int = re.search('([0-9X]{1,2})', str(reg[1]['chr'])).group()
# Compute the LD correlation with LD
......@@ -137,9 +137,3 @@ def generate_genome_matrices(region_files, reffolder, folder_output, prefix, suf
#fo_mat = "{0}/{1}_{2}_{3}.mat".format(folder_output, reg[1]['chr'], reg[1]['startpos'], reg[1]["endpos"])
#transform plink output to a compressed generate_sparse_matrix
#generate_sparse_matrix(fi_plink, fo_mat)
generate_genome_matrices("/home/genstat3/WKD_LUCIE/Data_test/All_Regions_ALL_ensemble_1000G_hg38_EUR.bed",
"/home/genstat3/WKD_LUCIE/Data_test/Panel_ref",
"/home/genstat3/WKD_LUCIE/Results",
"ALL_ensemble_1000G_hg38_EUR_chr",
"","\t")
\ No newline at end of file
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