1 files changed, 0 insertions, 122 deletions
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
deleted file mode 100644
index 2f917c71..00000000
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ /dev/null
@@ -1,122 +0,0 @@
-#!/usr/bin/python
-
-import sys
-
-# sys.path.insert(0, "..") - why?
-
-import os
-import collections
-import csv
-
-from base import webqtlConfig
-
-from pprint import pformat as pf
-
-from utility.tools import get_setting
-from wqflask.database import database_connection
-
-
-def show_progress(process, counter):
-    if counter % 1000 == 0:
-        print("{}: {}".format(process, counter))
-
-
-def get_strains(cursor):
-    cursor.execute("""select Strain.Name
-                      from Strain, StrainXRef, InbredSet
-                      where Strain.Id = StrainXRef.StrainId and
-                            StrainXRef.InbredSetId = InbredSet.Id
-                            and InbredSet.Name=%s;
-                """, "BXD")
-
-    strains = [strain[0] for strain in cursor.fetchall()]
-    print("strains:", pf(strains))
-    for strain in strains:
-        print(" -", strain)
-
-    return strains
-
-
-def get_probeset_vals(cursor, dataset_name):
-    cursor.execute(""" select ProbeSet.Id, ProbeSet.Name
-                from ProbeSetXRef,
-                     ProbeSetFreeze,
-                     ProbeSet
-                where ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
-                      ProbeSetFreeze.Name = %s and
-                      ProbeSetXRef.ProbeSetId = ProbeSet.Id;
-            """, dataset_name)
-
-    probesets = cursor.fetchall()
-
-    print("Fetched probesets")
-
-    probeset_vals = collections.OrderedDict()
-
-    for counter, probeset in enumerate(probesets):
-        cursor.execute(""" select Strain.Name, ProbeSetData.value
-                       from ProbeSetData, ProbeSetXRef, ProbeSetFreeze, Strain
-                       where ProbeSetData.Id = ProbeSetXRef.DataId
-                       and ProbeSetData.StrainId = Strain.Id
-                       and ProbeSetXRef.ProbeSetId = %s
-                       and ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId
-                       and ProbeSetFreeze.Name = %s;
-                """, (probeset[0], dataset_name))
-        val_dic = collections.OrderedDict()
-        vals = cursor.fetchall()
-        for val in vals:
-            val_dic[val[0]] = val[1]
-
-        probeset_vals[probeset[1]] = val_dic
-        show_progress("Querying DB", counter)
-
-    return probeset_vals
-
-
-def trim_strains(strains, probeset_vals):
-    trimmed_strains = []
-    #print("probeset_vals is:", pf(probeset_vals))
-    first_probeset = list(probeset_vals.values())[0]
-    print("\n**** first_probeset is:", pf(first_probeset))
-    for strain in strains:
-        print("\n**** strain is:", pf(strain))
-        if strain in first_probeset:
-            trimmed_strains.append(strain)
-    print("trimmed_strains:", pf(trimmed_strains))
-    return trimmed_strains
-
-
-def write_data_matrix_file(strains, probeset_vals, filename):
-    with open(filename, "wb") as fh:
-        csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL)
-        #print("strains is:", pf(strains))
-        csv_writer.writerow(['ID'] + strains)
-        for counter, probeset in enumerate(probeset_vals):
-            row_data = [probeset]
-            for strain in strains:
-                #print("probeset is: ", pf(probeset_vals[probeset]))
-                row_data.append(probeset_vals[probeset][strain])
-            #print("row_data is: ", pf(row_data))
-            csv_writer.writerow(row_data)
-            show_progress("Writing", counter)
-
-
-def main():
-    filename = os.path.expanduser(
-        "~/gene/wqflask/maintenance/"
-        "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2"
-        "(Oct08)_RankInv_Beta.txt")
-    dataset_name = "Eye_AXBXA_1008_RankInv"
-
-    with database_connection(get_setting("SQL_URI")) as conn:
-        with conn.cursor() as cursor:
-            strains = get_strains(cursor)
-            print("Getting probset_vals")
-            probeset_vals = get_probeset_vals(cursor, dataset_name)
-            print("Finished getting probeset_vals")
-            trimmed_strains = trim_strains(strains, probeset_vals)
-            write_data_matrix_file(trimmed_strains, probeset_vals, filename)
-
-
-if __name__ == '__main__':
-    main()