From f560cd7837d311525741ba540623a9fa97342b95 Mon Sep 17 00:00:00 2001 From: Lei Yan Date: Wed, 5 Feb 2014 13:14:22 -0600 Subject: On branch master --- wqflask/maintenance/dataset/.gitignore | 2 + .../20140110_Megan/C57BL-6JxC57BL-6NJF2.geno | 69 ---------------------- .../maintenance/dataset/20140110_Megan/conf.ini | 5 -- wqflask/maintenance/dataset/20140110_Megan/run.sh | 1 - wqflask/maintenance/dataset/datastructure.py | 2 +- wqflask/maintenance/dataset/run.sh | 1 - wqflask/maintenance/dataset/specials.py | 56 ++++++++++++++++++ 7 files changed, 59 insertions(+), 77 deletions(-) create mode 100644 wqflask/maintenance/dataset/.gitignore delete mode 100644 wqflask/maintenance/dataset/20140110_Megan/C57BL-6JxC57BL-6NJF2.geno delete mode 100644 wqflask/maintenance/dataset/20140110_Megan/conf.ini delete mode 100644 wqflask/maintenance/dataset/20140110_Megan/run.sh delete mode 100644 wqflask/maintenance/dataset/run.sh (limited to 'wqflask/maintenance/dataset') diff --git a/wqflask/maintenance/dataset/.gitignore b/wqflask/maintenance/dataset/.gitignore new file mode 100644 index 00000000..4910042e --- /dev/null +++ b/wqflask/maintenance/dataset/.gitignore @@ -0,0 +1,2 @@ +*.pyc +datadir/ diff --git a/wqflask/maintenance/dataset/20140110_Megan/C57BL-6JxC57BL-6NJF2.geno b/wqflask/maintenance/dataset/20140110_Megan/C57BL-6JxC57BL-6NJF2.geno deleted file mode 100644 index f0c05a3a..00000000 --- a/wqflask/maintenance/dataset/20140110_Megan/C57BL-6JxC57BL-6NJF2.geno +++ /dev/null @@ -1,69 +0,0 @@ -###Created by M.K.Mulligan 04242013 -###B=C57BL/6J; N=C57BL/6NJ; H=heterozygous or N on the X chromosome for males; U=No call -@name:C57BL-6JxC57BL-6NJF2 -@B=C57BL/6J; N=C57BL/6NJ; H=heterozygous; U=No call -@type:intercross -@mat:B -@pat:N -@het:H -@unk:U -Chr Locus cM Mb C57BL/6J C57BL/6NJ JxNJ0000 JxNJ0751 JxNJ0752 JxNJ0753 JxNJ0783 JxNJ0801 JxNJ0802 JxNJ0804 JxNJ0806 JxNJ0807 JxNJ0809 JxNJ0810 JxNJ0811 JxNJ0812 JxNJ0813 JxNJ0814 JxNJ0815 JxNJ0816 JxNJ0817 JxNJ0818 JxNJ0819 JxNJ0820 JxNJ0822 JxNJ0823 JxNJ0824 JxNJ0826 JxNJ0828 JxNJ0829 JxNJ0830 JxNJ0831 JxNJ0832 JxNJ0833 JxNJ0834 JxNJ0835 JxNJ0836 JxNJ0837 JxNJ0838 JxNJ0839 JxNJ0840 JxNJ0841 JxNJ0842 JxNJ0843 JxNJ0844 JxNJ0845 JxNJ0846 JxNJ0847 JxNJ0848 JxNJ0849 JxNJ0850 JxNJ0851 JxNJ0852 JxNJ0853 JxNJ0854 JxNJ0855 JxNJ0856 JxNJ0857 JxNJ0858 JxNJ0859 JxNJ0860 JxNJ0861 JxNJ0862 JxNJ0863 JxNJ0864 JxNJ0865 JxNJ0866 JxNJ0867 JxNJ0868 JxNJ0869 JxNJ0870 JxNJ0871 JxNJ0872 JxNJ0873 JxNJ0874 JxNJ0875 JxNJ0876 JxNJ0877 JxNJ0878 JxNJ0879 JxNJ0880 JxNJ0881 JxNJ0882 JxNJ0883 JxNJ0884 JxNJ0885 JxNJ0886 JxNJ0887 JxNJ0888 JxNJ0889 JxNJ0890 JxNJ0891 JxNJ0892 JxNJ0894 JxNJ0895 JxNJ0896 JxNJ0897 JxNJ0898 JxNJ0899 JxNJ0900 JxNJ0901 JxNJ0902 JxNJ0903 JxNJ0904 JxNJ0905 JxNJ0906 JxNJ0907 JxNJ0909 JxNJ0911 JxNJ0912 JxNJ0913 JxNJ0914 JxNJ0915 JxNJ0916 JxNJ0917 JxNJ0918 JxNJ0919 JxNJ0920 JxNJ0921 JxNJ0922 JxNJ0924 JxNJ0925 JxNJ0926 JxNJ0927 JxNJ0928 JxNJ0929 JxNJ0930 JxNJ0931 JxNJ0932 JxNJ0933 JxNJ0934 JxNJ0935 JxNJ0936 JxNJ0937 JxNJ0938 JxNJ0939 JxNJ0940 JxNJ0941 JxNJ0942 JxNJ0943 JxNJ0953 JxNJ0954 JxNJ0955 JxNJ0956 JxNJ0957 JxNJ0958 JxNJ0959 JxNJ0961 JxNJ0963 JxNJ0964 JxNJ0965 JxNJ0966 JxNJ0967 JxNJ0968 JxNJ0969 JxNJ0970 JxNJ0971 JxNJ0972 JxNJ0973 JxNJ0974 JxNJ0976 JxNJ0977 JxNJ0978 JxNJ0979 JxNJ0980 JxNJ0981 JxNJ0982 JxNJ0983 JxNJ0984 JxNJ0985 JxNJ0987 JxNJ0988 JxNJ0989 JxNJ0990 JxNJ0991 JxNJ0992 JxNJ0993 JxNJ0994 JxNJ0995 JxNJ0996 JxNJ0997 JxNJ0998 JxNJ0999 JxNJ1000 -1 1-59904011 x 59.904011 B N N H N N H B H N B N H H H H B H N N H H N B H H N N B H N H H H H N H B H H B H H H N B H H H H N H B N H H H H H H N H N H H N H N H H B H H H N H B H N B H B B H H N H H H N H H H H H H H N B H B B B H N B N B H N B B H H B B H H B H B N B N B N N N B B H H B H H H B H B N H N N H B H H B H H H B B H H N H H H B N N H N N B B N N H N B H N H B H H H B B H N H -1 1-90703267 x 90.703267 B N N N N N H H H N H H H H H H H H N N H H H B H H H N B N N H B H H H H H H H B H H H N B H N N H N H B N H H H H H N N N H H H H H B H H B H N N N H B H H H H B N H H N H H B H H H B H H H H N B N H B B H N B N B H N B H H B H B H H H H B N H H H N H H B B H H N H H H B H H H H N N H B H H B N H H B B H H N H H H H H H H H N H B N H H N B N N N B H H H B B H N H -1 rs51237371 x 183.248134 B N H N H N N B B N H H H H H H N N B H N H H B B H H H B H N H B B N N N N B N B H B H N N H H H B N H B H B H H B H H H H H H N H H B H H H N H N H H B H N B H H H N H N H H H H B B B H H N H H H H N N B H B B H B H H B N H H B H B H H H H H H B N H B H B N H H H B B B H B N B H H N N N N H B H H H H H H N N H N H H H H H B H H N B B H B B B N H H H H N B H H H N -2 2-24042711 x 24.042711 B N H H B B B H H N N H H H H N H B N B H H B H H H H N N B H H B B H B B H B B H N B H N N N H H B N H N B N H H H B H B B H N B B H H H H N B N H H H H H U B H H H H H H N H H H H B B N H H H H N B B B H N H H H H H H N H N B H H B H B N N H H H H N N N H H N H U N H B H H B H H H H N H N N H H H N B H N B H H H H B N H H H N B B B N N B H N N H H H H N N H H B B -2 2-59889445 x 59.889445 B N H N B B B H H N H N N H H H N H N B N B H B N B H N N H H H H H N H B H B N N N B H N H N H B B N H H B N H H H B H B H H N B B B H B H N B N H N N H H H B H H H H N N H N H B H B B N H B H H H H B B H H H H H H H H N H N B H B H N B N N H H H H N N N N N H B H N H H H H B H H B H H N N N B H B N H H N B H H H H B N H H H H H H B H N H H N H H B H H H N H N H B -2 2-152607139 x 152.607139 B N H N H B H N N N H N H H B N H H N N N H B H N H B H N H N B H N N H B B B H H H B H N B B H B H H H H H H H H H B B B H H B B B B H N N H B N B H N N H H B H H B H N N H H N N B B B H N B H N H N B H H H B N N H N H N N B B H H N N N H H H N N H N N H N N H B H H B N H H B N H B H B H B H B B B H B H H H H H H H H H N H B H B H N N H H N H H H B B H H H H H H H -3 rs30751697 x 54.718828 B N H B N H H H B H B H H H B H N H N B H N N B H H B N B B H N H B B H N H H N H H B H H H H H N B H H H B B H N H H N N N H H N N B N B B N H H H H H H H H H B H H N H N H N H H N B H B N B B H B H B B H B H H H H H B H H N B B H B H H H N H B B N N H H H H B B H H H H N N H H N H B B H B B H B N H B H N H H N H H B H B H B H H N B B H H B B B N H N N H B B H H N -3 rs13474735 x 95.538799 B N H B N H H H H H B H N B B H N H N H B N N B H N H H B B H H H B H H H H H N H H B B B H H H N B H N B B B H N H B N H H H H H H B N H H N H H H H H H B N H B H H N H H H H H H N H H H N B B N B H H B H B H B B H N B H H H H H H B H H N N H B B H N H H H H B H H H H H H N B H N H B H H B B N H N H B H N H H N H B H N B N B H H H B B N B B B H N H N N H B H N H N -3 3-159474065 x 159.474065 B N B N N B H B N H N H H N B B N N N H B H H B B H H B H B H H B B N H H N N H N H H B H N H B H H H N H H H N H H B N H H H H H H H N H H B N B H N H B B N B H B H B H B B H H B H H N B N B H N H H B H N N B B B N N H N H N N H N B B N H H B B B B B H B B B N N N H H N H H H B H B B H B H H H N H B B N H N H B B H N H B N H H B B N N N B N H B N H H H B B H N H H -4 rs13460207 x 21.800831 B N H H H H N B H H N N H H B H N N N H B H N H N B B H U B H B H H H N B B H B H B H B N H H H H N B H H B H N H B B H B H N N H N B B N N H N N N H H N N U H H H H N N B B H H H N H N H B B B H H H H H H B H H B H B B H B H H N H H H H B H H H H B N U H H B B B U U N H H B N B N H N H N H N N H B H B H N B N N H H N B H N N H N N B H H H B H H N H N H B H H B U B -4 rs46850777 x 40.752043 B N B N B H N B H H N N B B B H N N H B B H B H N B B H N B H B B N H N B B H B H B H B N H B H H N B B H B H H H B N H B H N H H N H B N N H N N N H H N H H H H H H N N B B H H H N H N H H B B H H H H H H B H H B H H H H B N H N B H H H B H H H H B N B H H B B B H N N H H B N B N H N H N H N N B H H B H N B N N H H N B H N H B N N H H H H H B H N H N H B H H B H B -4 rs32865425 x 124.331809 B N B N H N B H H H N H H H B H B H H B H H B H H B H N H B H B H H H N H B H B B B N B N H B H H N H H B H B H H B N H H H N N H N H B N H H H H H H N H H B N H H H B H H B H H H N B H H H B H H B N N H B H H H N N H N H B N B B B B B N H H B H H B N H N B H B B H H H N H H B B H H N H N N N N B N B H H N N H H N N N B N H H B H N H H N H N H B H N H N B H H H H H -4 4-137777588 x 137.777588 B N H N H N B H B H H B H N H H B H H H H H H H H H H H H B H B N H H H B H H H H B N B H B H H H H H H B H B B H B N H H H H N H N H H N H H H H B H N H H B N H H H H H H B H N H N B H N B B H B B N H H B N B H N H B N H B N B B N B B N H H B H H B N H N B H H H H H H N H H B B H H N H H N N N B N B H H H N H H B N N B N B H B H H H H H H N N H H N H N B H H N H H -4 rs32407463 x 150.05969 B N H H H N B N B B H B H N N H H H H H H H H H H H H H U H H B N B B H B H H N H B H B H B H H H H H H B H B B H B H H H H H N H N H H H H H H H B B N B H U N N B H H B H B H N H N B H N B B H B B N H H H N B H N H B N H B N B B N B B N H B B H H B N H N H H H H U H H H N H B B B N N N H N B N H N B H H H N H H B N N B N B N B H H H H H B H N H H H N N B H B N U H -5 rs33209545 x 60.224881 B N B H H H N H H B H N H H B H H H N H N B N H H N B H H H H B H H B N N H B H N H H B H B B N B H N H H H H H H B N N H H B H H H N H B H H B H N B H H H H N H B B H N N B N H H B H N H H B B H H H N N H N H B H H H H H N H B N H H B N B N N H H B B B N B B N H B N H H B H H H B B H N B B N H B N B N B N H B H H N N N N N N H N H N N H H N H H H H H H H H H B H B -5 rs29547790 x 71.32277 B N H H H H H H H B H N H H B H H H H H N B H H H N B H H H H B H H B N N H B H N H H B H B B N B B N H H H H H H B N N H H B H H H N H B H H B B N B H H H H N N B B H N N B N H H H H N H H B B H H H N H H H H B H H H H H N H B N H H B N B N N H H B B B H B B H B B N H B B H H H B B H N B B H B B H B N B N H B H H N N N N N N H N H N N H H N N H H H H H H N H B H B -5 5-90204376 x 90.204376 B N H H H H H B H B H N H H B H H H H H N H N H H N B H H N H B H H B N N H B H N H H B H H B N H B N H H H N H H B N H H H B H H H N N B H H B B N B H H H N N N H B B N H B N H B H H N H H B B B H H N H H H H H H H H H H N H B N H H B N H N N H H B B H H B B H B U U H H B H H N H B H N B B H B B H B N B H H B H H N N N N H N H N H N N H N N N H B B H H H N H B H B -5 rs3719791 x 132.016906 B N H H H B B B H B B H H H B H B N H H H N N H H N B H H N H H N H H H N H B H N H H B B H B H H B N N H H N N N H N H H N H H H N H N H B H B H N H H N B H B N H H H H H B N N B N B H N H B B B B H N B N H B H H N H N H N H H N B B H N H N N H H B B H H H B H B B N H H H N B H H H B H H B H B B B H H H N H B H H H N N H B B H N H B N B H H N H N B H H H N H B H B -5 rs33404968 x 149.838448 B N H H B H B H H H B N N H B H B H H H H N N H H N B H B N H N N H N H H H B H N H H B B N B H N B N N B B H H N H H H H N H H H N B N N B H H H N N H H H N B B N H N B H B N N H N B B H B B H N H B H B N B B H B N B N H N H H N B B H N H N H H H B B H H N B H B H N H H H N B H N H B H N H H H B H H H H N H B H H H H N H H B B N H B N B H H H H H B H H B N H H H H -6 rs30899669 x 39.350455 B N H N B H H B B B B N B H N B B B B H H H N B N H B B B H H H H H H B B N H N N H B N H H B N H H H H H H H B H N H B N N H N N H N H B N N H H H H B N N B H H B H N H H N H H H B H B H N N B H H H H H B B H B H H N N N H H B H H B H B N H N H H B N B N H B H H H B H H H B H H H B H B B B N N B N H B H B B B N H H N B H H H B B N N H H B N H H H H B H N H B N B N -6 6-90109621 x 90.109621 B N N N B B N B B B B N B B N H H H B B H H N B H N B B B H H N H H H H B N B N N H H N H N B N H H H H H H N B H H B H N H H N N H H N H N H N N H N B N H H H H B N N H H H H B H H H B H H H B H H H H H B B H H H B N H N H B N B N H B H N H N N N N N B N N B H H N B H H H H B B H H H H B B B N N H B B N B H H H H H H H H H H H H N B H N H N B N B N H H N H B H H N -6 rs30119689 x 145.19523 B N N N H B N B H H B H H B B N B H B N H N N B H H H B B B H N N H N N H N H H N N N H H H H N H H H H H H N B N N B H H B H H N H H N H H N H N B N H N H H H H B N N B H H B B B B H H H H B B B B H B B B N H H B B N B B H H N H H H H N N B H N H N N H H B H B B N H H B H B B B H N N B B H B B N H H B B H H H B B B H H H N H N N B H N N H H H N B N N B N N B B N B -7 rs3148686 x 31.091494 B N N H H B B H H H H H B H N N H B H N H H H H H N H H B H H H N H B H N H B B H N H B B H N H N H H H N H H N H H H H H H H B H H H B N H B H N H H H B H B H B N H H N B H H N H H N N H H H B N B B H H B B H N H H N H H N N N B H H B N H H H H N B B H B H B B N N B H N H H H H H H B B B H N B H H H B B N H H B N H H N B H H N B H H B H H H B B N B H H N H N H H N -7 rs50155421 x 63.386662 B N H H N H B H H H B H B N N N H B H H H H B H H H H H H B H H N H B H H B B H H N H B B B N B H H N H N H B N H B N B H H H B H H B B N H B H H H H H H H B H B N N H N H N B H H H B H B H H H H B B H H H B B N B H N H H N N N B H H B N H H B H H B B H H B B B H U H H N H H H B H H H B H H N B H H H H B H H N H N B H N B H H N H H H B H H H N B N B H H N H N H H N -7 7-127278693 x 127.278693 B N H B N H B B B H B N B N H H H B H H N N B B B B H B H H N H H N N H H H B H B H H H B B H H H H H N N B H N B H N H B N N H H N H H N H H H B H H B N B H H H N H N H H H B H H H B H B N B H H H H B H H H B H H H N H H B N H B H B H H H H B H H H B H H B H N B H H H N H H H H H B H H H N N B H N N H H H B N N N B H N H H B N H H N B B B H N H N H N B H H N H N H -8 8-14127388 x 14.127388 B N N H H H H N H B N H N B B H H B H N H H H N B B H H N B H H H B B H B H N H H H H N H H H B B H H B N N H N H B N N H H N H H H B H B N H H N H N H H N H H N N H H B H H B N H H H H B H N H B N N N H H N H N N H H H H H N N H B B B H H H N H B H H H B H B B N N H B H B B B H B H B H N B N B N H B N H B H N H H H H H B H H H H H H H N N H H N B H N H H H N H H H -8 8-61604358 x 61.604358 B N N H H H B N H H H H N H B B H H H N H H H H H H B B H B B H N H B H H H N H H N H H N H H H H N B B H N N N B H N H H B N H N H B H N H H H H H N H H N H H H N H B H H N H H H H H H H H N H B N H N H H N N N N N H B H B H N H B B H H H N B H B B H B B H B H N H H H B H H B H B N H H N B H B N H B H H B H H H N H H N H N H H H B H H N B N H N H B N H B N H H N N -8 8-87889078 x 87.889078 B N N H H H B H H H B H N H B B H H H N B H N H H H B U U B B B N H B H H H N H H H H H N B B N H N B H H N N N B H H H H B N H N N B H N H H H B H N H B N U H H N H B H B N H B H H H H H H N H B N U N H H N N N N N H B H B B N H B B H H N H B H B B H U B H B N N U U H B H N B H H N H H N B H B H H H B H N H H H N H N N N N H H H H H H N B N H N H B H H B N B H U N -8 8-122469661 x 122.469661 B N N N U B H B H H B U B H H U H H H H N H B U H H B U U N B U U N H U N H H H H N B H B B N N B H N H H H H N B H U H H U N H H H B H N H H B B B N H B H U H H B B H H B B H H B H H H H N N N H N U H H B N H N N H H H H B B N H H B H B N H B H B H H U N H H H N U U H B H N B B B H N H N H H B H B H B H N B H B H N N N N H H B H N H B N H H N N H B H H B H H H U N -9 9-3994759 x 3.994759 B N B N N H N H H N B B H N B H B N H H N N B H N H H H H H H H H B N B H H H H H B H H H N H H H B B N B B B H H H H B B H B H H H H B N H N H N B N H H H N H B N B H H H B B H H H N N H B H B H N B N B N H H H H H H H H H B B N N B H H H H H H H B H H H N H H B B N H B H B H H B N N H H H H B N H B N B N H H H H H H H N B H H N H H B H B H H H B B N H B N H B B H -9 9-24935069 x 24.935069 B N B H N B N H N N B B H N B H B H H H N N B N N H H H H H H H N B N B H N H H B B H H H N H N H B B N B B B H H H H B B B B H B H H B N H N N H B N H H H N H B H B B H N B B H H H N N H B H B H N B N B N H H H N N H H H H B B H N B H H B H H H H B H H H N H N B B N H B H B H N H N N H H B H B N H B N B H H H N H B H H N B H B N H H H H B H H H B B N H B N N H B H -9 rs30522453 x 86.11453 B N B H H B N B N H B N B H H B B H B H N H N N B B N H N H H N N H H B H N N N H H H H N H H H H N B B B B H B B H H N H B H H B H H H H H N N H B H B H B H H H H H B B H H B N H H B H N B N H N H N H B H B N H H H B N N N N H N N B H H H H H H B H H H N N N H H H B B H N H B H H H B B N B H H N N B B H H H N N B B N H H B H B H H N H H B H H N H B N H H N H N U H -9 rs49019729 x 119.926025 B N B N H H N B B B H H N H H B H H H N N H N B B B N H H H H N N H H H H H N N H B H H N H H H H N N B B H N B B H B N B B H H H N H B N H H B H N B B H B H B B H H B H H B H N B B N H N B H N N B N H H H H H H B H H H H N H H N H H N H H H H H B N N H N N H H H H B B H H H H H N H B B N N B H B N H B H H H N H B H N H H B B B H H H H H H N H H B H H H H N B N H H -10 rs29330320 x 29.332472 B N N B N N H H N B B U N B B U B B B N N H N N B B B U U N H N H H H H H H N B B H B H B B H B H N N H N N B H H B U N H H H N B H H H H B H B H H N N H N U N H B N H H B B H H H H H N H N H H H H H N H B H N B B B H H N B B H N H B H H N B B N H H B N B B N B N U U H H H H H H B B B N H H H H N B H B N B H H B B H H H H H H N B B B B N N H B H B H H H B H B N U H -10 rs13480628 x 66.700922 B N N B N N H H N B B H N B B H H B B H N B H N B B B B N N B N H H H H N N N B B N B H B B H B H N N H N N B B H H B H B H H N B N N H H B B B H H N H H N H N H B N H B H B H H H H H N H N H H H B H N H B H N H B B H H N B B H H H B H H N B B N H H H N H B N B N H H H H H B H H B B B N H H H H N B H B N H B H B H H H H H N H H B B H B N H H B H B H H H H N H H U H -10 10-87554578 x 87.554578 B N N B H N H H N B B B N H B H H B B H N B H N B B H H N B B N B H H H N N N B B N B N H H H B N N N H N N B B H H B H B N H N B N N N B B B B H H N B H N B N H B N H B H B H H H H H N H N N H H B B N H B N N H H H H H H B B H H H B H H N B B N B H H N H H N B H H B H N H B H H B B B N H H H H N B H B N H B H B H H H H H N H H H B H B N H H H H B H N N H N H H B H -11 rs48169870 x 30.575691 B N B U U H H H B H H U N H B U N B H N B H N U H H N U U H H U U B B U H U H H B H H B B H B N H H H B H H B H H B U U H H B B B H H N H B N H B B H H B B U H H U N N B N H H B H B B B B N H H H H U H H H H B H H H H N N H N H H H U U B H N H B B U H H U H N H B U U H H N N N N N H H H H B H B H H B H H N H B H H H U H H H H B B H N H N H B B H H N N B H N H H U N -11 11-46036117 x 46.036117 B N H N H H H B H H H N N H B N N B H N B H N H H N N B H H H B B B H N H N B H B H H B B N B H H H H B H H B H H H N H H N B B B H H N N B N H B B H H B H N H N N N N H N H H B H H B B B N H H H H B H B H H H H N H H N N N N H H H N N B H N H B H H H H N H H H B B N H H N N N N N N B H H B H H H H B H H H H B H H H H H H H H B B H N H H H B B H N N N B H N H H H N -11 rs6268547 x 62.886983 B N H H H H H B H H H N N H B N N B H N H B H B N N H B H B H B B B N N H N H H B H H B H N B B H H H B H H B H H H N H H H B H B H H N N H N H B B H H H H N H N N N N H N B H B H H B B B N H H H H B H B H H H H N N B N H N B N H H N N B H N H B H H N B B H H H B H N H H N H N N N N H H H B H H H H H H H B H H H H H H H H H H B H H N H B H B B H N N H B H N N B H H -11 11-90341985 x 90.341985 B N H B H H H B H H N N N N B N N H H H H B H B N N B B H B H H B B N N H H H H B H H B H N B H H H N N H H H H N H N H H B H N B H H B H H N H B H B H H H N H H H H N H H B H B H H H H H N H H H B B H B H H H H N H B N H N B N H B N H B H N B N H H N B B H H N B H N B H N H N N H N N H H H H H H B H H H H H H H H H H H B H H B H H H H B B B B H N N H H H N N B H B -11 rs49027247 x 120.168102 B N H B H H H H H H N H N N H H N N B H H H H B N N H B N B N H B B N N H H H N B H H H H H B H H N N N B H H H N B H H H B N N H N B B H H N H H N B N N B N N H B B N H H H N H N H H H N H H B H B B H N H H B H N B B H N N H H N H N H H H H B N H H H H B H H H H H N B H H H H H B H N B N H B N H H B H H B H H H B B N N B N H H H B B H H B H B B H H H H B N N B H B -12 rs29165094 x 29.094628 B N H N B B H H H H B B H B N B H N N H H H N H H H N B N N N B H H B H N H H H B N N B H B H H H B N B H H N H B H B H N H H H N N H N H H B H H B N N B B N N N B B N B B H N B H H N H N H H H H H N H H N H H H B B B N B B H H N H H H H H N B N N H H N H N B B N H N N H N B H H B B H H B B H H N N B H H H H H H B N H N B H B B N B H B N B B H H H B B H B N H N H N -12 12-92834114 x 92.834114 B N H H B H H H N H B B H N N N B N N H H B N H H N H B H H N H N B B H N H N H B N H B H B N H N H H B B N B H B H H B B H H H H N H H H H H H H B H N B H N H N B B N B B H N B N H H H B N B H H B B H B N N H H B B B N B B N H N B H N B H N B N N H H H H H H B H B N N H H N H H H H H B H H H N N H H N B H H N B H B N H B N B H N B H H N B H H H H H B H B H H B B H -13 rs29248623 x 52.853421 B N N N B H H N B H N N H N B B H H B N H B B B H N H H N B H H H H H H H N H B H H H H B H N N N H B H H H N H H H H B B H H H N H N H H B H H N H N N B H H H H B N B H H H B N B N H B N B H N H H N B N N H H N N B H N B H H H H B H N N B N N H H H H B B B N H H N H N H H B H B H H N N N B B H B N H B N N N H B N H N H B B N H B N B H B B N B N H B H B N H H N H B -13 rs29622109 x 88.566525 B N H H B H B H H H N N H N B B B N B N N H H B H N B U U B H N N N H N H N H B H H H H B H N N N H B B H H H B H H H B B B B B N H N H H B N H N H N H B H U N B B N B H H H B N B N H H N B H H H H H B N N H H N N B H N H H B B N B H H H N N N H H H H U B B H B H U B N H H B B B H H N H N B B H B H B B H H N H B N B N N H B N H H N H B B B N B N H B H B N H H N U B -13 rs29235721 x 119.932328 B N H B B B B H H H H N H N B H H N B N N H H H H N B B N H H N N N B N H H H B H H H H B H H N N H B H B H B B B B N H B B B B N B N N N N N H N N H H B H B H B B H H N H B H N N N N N H H H B H H B H N N N H H H B H H N H B B N B N H H H N N N H H H H H B B B N B B H B B B B H N H N H N B H B B H H B N H H H H H H H N H B N N N N N H H H N H B H H N H H H H H H B -14 14-91246882 x 91.246882 B N H N U H B H H H H N N H B B H N H H H B H H H N H H B B H N H B B N B H H B H B H H B N H H H N B B B N H B H B B B B N B H B H B B H B H N H H N H N B B B H B B H N H N B N B N N H B B N B N B B N N H H N B H H N N H H B B N H B H H H H H N N H N B N B H N B B U H B N B H B H H H H H H H B B B N H H N B B H H N H B H H H H H H B H H B H B N B B H B H H B H H B -14 14-117002819 x 117.002819 B N H H H H B B H H H N H H B B H N B H H B H H N H H H B B H N H N H N B H H H H B H H B H H H H N B B H B H B B B B B B N B H B H B B B B B N H H B N H H H H H B B H N H N B N B N N N B B N B N H H N N H H H H B H N N H H B B N N B H B H H N N H H N B N B H N H B H B H N B H B H H H H H H H B B B N B H B B B B H N N B H H H H H H B B H B H H N H B N B H H B N H H -15 15-11266138 x 11.266138 B N N H H B N N B H H B H H N N H B H H H H H H H B H U U H H B B N H B B N H N H N N H H H H H B B H B N N H H H B B N H B B H N B N H H N B H N B B N H H U N H B H N B N B H B H B H H H B N B H H N N B B B N N H H B N H H B H H H B B B N H H H B H H U H N B N B U U H N N B B H B B H N H H H H N N H H H N B B N H H B H H H H H N B N N H N H H H H N N H B H H H U H -16 16-35291630 x 35.29163 B N H H B B H H H H B H H H H H B H N B H H H B H B H H H H H N H B H B N H H N N B H N H H N H B N B N H H B H B H B H H H N H B H H N H B N H B H N H B H N N H H H H N B H N H B H H B N H H N H B N H B H B N H H H B N N N N B B H N H B N N N N N B B H H H B N H H B H H B H N B N H N H H H H H B N N H B N B H N B H H B B N N H N H B B B H N H N N N B B N N H B N B -16 rs48691087 x 60.954442 B N H H B B B H H H H H H H H N B H H B H H H B H H H H H H H N H B H B N B H N H B H N H H N H B H H N H H B B B N B H H H N H B N H N H H N H H H N B B B N N H H H N N H H N H B H H B H H H N H B N H B H H N B H H B H N N N H B H N H B N N N H N B B H B H B H H H B H H H B H B N H N N N N H H B N N H B N B N N B H N H B N N H H B B B B H N H N N N B B N H H B N H -16 rs4217166 x 90.181254 B N H H U B B B H H H U H H H U B H H B H H H U H H H U U B H N U B N B N B H N U H H N B H H N B H H H N N H U B H U H H U H N B N U H H H H H H H N B B B U N N U H N N H B N B B H H H B H H N N H U H B H H H B B B B H N N N H H N N U H N N N H H B H U U H B H H U U U B H B B B N B N N N N N H H H H H B H B N N B H N H B H N H H B H B B H N H N N N B H H H H H U H -17 rs46703123 x 26.991191 B N H B H N H B H H N B B H B H H N B N B N N H H H N H B H N B N H H H H H H N H H H H N N N H H N H H H H H N H B N H H B H H N H H H B H H H N H H B B H N H N B H H H N B H H N H H H H H B B H H H N B N B H B N H H H B N B N H H B N B B H B H N N N N B N H H H N B H H N H B H H B N B B B H H B H B B H N N H B H H H N H H H N H B B H N H H B N B N H H H N N N B H -17 rs33387924 x 68.102223 B N H H H N H B N H H H H H B H B H H N H N B N H H N N B H H N N B H N N B B B H N N H N H H H H N H H H H B N B B H H N H B H N H H H B B B B N B H H B B H B H B H N B N H H N N N B H B H B B B H H N B H H B H H H H N B N B B H H N N B H H B H N H N B H H H N H H H N H N H B H H H N B N B B N B B N B H H N H B H H H H H H N N B H N B N B H B H H H B H N H N N B H -17 rs50807504 x 90.107756 B N H H H N H H N H B H U N B N B B H H H N B N H N N N B N H N H H B N N B B H N N H H N B H H B B N H H H B B B N H B N N H N N N H B B H B H N H H H H B B B H B B N H H H H H N H B B B N B N B H H B B H N H H H B H N N N N B H H N H B N B H H H H H B H H B N H H H H H N N B H H H N B N B H N B B N H H N N N B H H H H B N N N H H N B N B N B H H B B H H H H H B N -18 18-90618149 x 90.618149 B N H N H N H B H H N B N B H H N B H H H N H H B N H N H H H H N H H N H H N B N N B B H N H N B H H H N B H H N H H H B H H N N B B N H H H H N N B B H B H B B H N H H H H N H H H H N B N H B B H H H N B H H B N N N H H H B H H N H B H N B N B H H N H H B H H N N H H H N N N B H B N B H H H H B B H N N H B H B H H H H B H H H H B N H B H B H H H B N H N B N B N H -X X-61565614 x 61.565614 B N B B H H B B H H B H B H B B H B H B H B N B B B B H H H B B H B B H H B B H B H H H B B H H H B B H H H B H B H H B B H H H H B B B H H B H H B H B H H H H B B B H H H H H H H B B H B B H H H B H B H B B H B H B B H B B B B H H H H H H H B H B B H B H H B H H H H H B B B N B H B H H H B H B H B B H H B H B H H H H B H B B B H H B B B H H H H B H H H H B H B H B -X X-87964774 x 87.964774 B N B B H H B B H H B H B H B B H B H B H B N B B B B U U H B B H B B H H B B H B B H H B B H H H B B H H H B H B H H B B B H H H B B B H H B H H B H B H B H H B B H H H H H H H H B B H B B H H H B H B H H H H B B B H H B B B B H H H H H H H B H H B H H H H B B H B U H B B B N B H B H H B B H B H B B H H H H B H B H H B H B B B H H B B B H H H H B H H H H B H B U B -X X-149209478 x 149.209478 B N H B H B H B H H B H B H B B H B H B H H N H H H B H B B H B H H B B B B B H B B B H H B B H H B B H H H B H B B H B H B H B H B H H B B B H H B H H H B B H B B H H H H H H H H B H H B H H H H B H B H H H H B B B H B H H B B H H H H H H H B H H B H H B H B B H B B H B B B B N H B H H B H H B B H H B H H H B H B B B B H H B B H B H H B H B B B H B B H H H B H B B diff --git a/wqflask/maintenance/dataset/20140110_Megan/conf.ini b/wqflask/maintenance/dataset/20140110_Megan/conf.ini deleted file mode 100644 index 866373c2..00000000 --- a/wqflask/maintenance/dataset/20140110_Megan/conf.ini +++ /dev/null @@ -1,5 +0,0 @@ -[configuration] -speciesId = 12 -inbredsetid = 13 -genoFreezeId = 14 -genofile = C57BL-6JxC57BL-6NJF2.geno \ No newline at end of file diff --git a/wqflask/maintenance/dataset/20140110_Megan/run.sh b/wqflask/maintenance/dataset/20140110_Megan/run.sh deleted file mode 100644 index 44e96fd7..00000000 --- a/wqflask/maintenance/dataset/20140110_Megan/run.sh +++ /dev/null @@ -1 +0,0 @@ -/usr/bin/python ../code/genotypes_load.py conf.ini \ No newline at end of file diff --git a/wqflask/maintenance/dataset/datastructure.py b/wqflask/maintenance/dataset/datastructure.py index f94009f5..f27c1aab 100644 --- a/wqflask/maintenance/dataset/datastructure.py +++ b/wqflask/maintenance/dataset/datastructure.py @@ -1,6 +1,6 @@ import utilities -def get_probesetfreeze(inbredsetid): +def get_probesetfreezes(inbredsetid): cursor = utilities.get_cursor() sql = """ SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName` diff --git a/wqflask/maintenance/dataset/run.sh b/wqflask/maintenance/dataset/run.sh deleted file mode 100644 index eccfa507..00000000 --- a/wqflask/maintenance/dataset/run.sh +++ /dev/null @@ -1 +0,0 @@ -/usr/bin/python correlations.py conf.ini \ No newline at end of file diff --git a/wqflask/maintenance/dataset/specials.py b/wqflask/maintenance/dataset/specials.py index e69de29b..9caba879 100644 --- a/wqflask/maintenance/dataset/specials.py +++ b/wqflask/maintenance/dataset/specials.py @@ -0,0 +1,56 @@ +import datastructure +import genotypes +import probesets + +""" +For: Ash +Date: 2014-02-05 +Function: + For BXD group, calculate correlations with genotypes and probesets. +Running History: + 2014-02-05 /home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output +""" +def bxd_correlations(): + # + inbredsetid = 1 + genofile = "/home/leiyan/gn/web/genotypes/BXD.geno" + outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output" + # + t = genotypes.load_genos(genofile) + genostrains = t[0] + genos = t[1] + # + probesetfreezes = datastructure.get_probesetfreezes(inbredsetid) + print "Get %d probesetfreezes" % (len(probesetfreezes)) + # + for probesetfreeze in probesetfreezes: + # + print probesetfreeze + probesetfreezeid = probesetfreeze[0] + probesetfreezename = probesetfreeze[1] + probesetfreezefullname = probesetfreeze[2] + # + outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+") + outputfile.write("%s\t" % "ProbeSet Id") + outputfile.write("%s\t" % "ProbeSet Name") + outputfile.write("%s\t" % "Geno Name") + outputfile.write("%s\t" % "Overlap Number") + outputfile.write("%s\t" % "Pearson r") + outputfile.write("%s\t" % "Pearson p") + outputfile.write("%s\t" % "Spearman r") + outputfile.write("%s\t" % "Spearman p") + outputfile.write("\n") + outputfile.flush() + # + probesetxrefs = probesets.get_probesetxref(probesetfreezeid) + print "Get %d probesetxrefs" % (len(probesetxrefs)) + # + for probesetxref in probesetxrefs: + probesetid = probesetxref[0] + probesetdataid = probesetxref[1] + probeset = probesets.get_probeset(probesetid) + probesetdata = probesets.get_probesetdata(probesetdataid) + # + outputfile.close() + +bxd_correlations() -- cgit v1.2.3