Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

1 files changed, 0 insertions, 66 deletions

diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
deleted file mode 100644
index 9f01d094..00000000
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/usr/bin/python
-
-"""
-Generate relatedness matrix files for GEMMA from BIMBAM genotype/phenotype files
-
-This file goes through all of the BIMBAM files in the bimbam diretory
-and uses GEMMA to generate their corresponding kinship/relatedness matrix file
-
-"""
-
-import sys
-sys.path.append("..")
-import os
-import glob
-
-
-class GenerateKinshipMatrices:
-    def __init__(self, group_name, geno_file, pheno_file):
-        self.group_name = group_name
-        self.geno_file = geno_file
-        self.pheno_file = pheno_file
-
-    def generate_kinship(self):
-        gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \
-            " -p " + self.pheno_file + \
-            " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
-        print("command:", gemma_command)
-        os.system(gemma_command)
-
-    @classmethod
-    def process_all(self, geno_dir, bimbam_dir):
-        os.chdir(geno_dir)
-        for input_file in glob.glob("*"):
-            if not input_file.endswith(('geno', '.geno.gz')):
-                continue
-            group_name = ".".join(input_file.split('.')[:-1])
-            if group_name == "HSNIH-Palmer":
-                continue
-            geno_input_file = os.path.join(
-                bimbam_dir, group_name + "_geno.txt")
-            pheno_input_file = os.path.join(
-                bimbam_dir, group_name + "_pheno.txt")
-            convertob = GenerateKinshipMatrices(
-                group_name, geno_input_file, pheno_input_file)
-            try:
-                convertob.generate_kinship()
-            except EmptyConfigurations as why:
-                print("  No config info? Continuing...")
-                continue
-            except Exception as why:
-
-                print("  Exception:", why)
-                print(traceback.print_exc())
-                print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
-                                                                    convertob.latest_col_pos))
-                print("    Column is:", convertob.latest_col_value)
-                print("    Row is:", convertob.latest_row_value)
-                break
-
-
-if __name__ == "__main__":
-    Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
-    Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
-    GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
-
-    # ./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD