1 files changed, 0 insertions, 72 deletions
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
deleted file mode 100644
index 18fbb8a1..00000000
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/python
-
-"""
-Convert data dryad files to a BIMBAM _geno and _snps file
-
-
-"""
-
-import sys
-sys.path.append("..")
-
-
-def read_dryad_file(filename):
-    exclude_count = 0
-    marker_list = []
-    sample_dict = {}
-    sample_list = []
-    geno_rows = []
-    with open(filename, 'r') as the_file:
-        for i, line in enumerate(the_file):
-            if i > 0:
-                if line.split(" ")[1] == "no":
-                    sample_name = line.split(" ")[0]
-                    sample_list.append(sample_name)
-                    sample_dict[sample_name] = line.split(" ")[2:]
-                else:
-                    exclude_count += 1
-            else:
-                marker_list = line.split(" ")[2:]
-
-    for i, marker in enumerate(marker_list):
-        this_row = []
-        this_row.append(marker)
-        this_row.append("X")
-        this_row.append("Y")
-        for sample in sample_list:
-            this_row.append(sample_dict[sample][i])
-        geno_rows.append(this_row)
-
-    print(exclude_count)
-
-    return geno_rows
-
-    # for i, marker in enumerate(marker_list):
-    #    this_row = []
-    #    this_row.append(marker)
-    #    this_row.append("X")
-    #    this_row.append("Y")
-    #    with open(filename, 'r') as the_file:
-    #        for j, line in enumerate(the_file):
-    #            if j > 0:
-    #                this_row.append(line.split(" ")[i+2])
-    #        print("row: " + str(i))
-    #        geno_rows.append(this_row)
-    #
-    # return geno_rows
-
-
-def write_bimbam_files(geno_rows):
-    with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
-        for row in geno_rows:
-            geno_fh.write(", ".join(row) + "\n")
-
-
-def convert_dryad_to_bimbam(filename):
-    geno_file_rows = read_dryad_file(filename)
-    write_bimbam_files(geno_file_rows)
-
-
-if __name__ == "__main__":
-    input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
-    convert_dryad_to_bimbam(input_filename)