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authorZachary Sloan2013-04-11 20:08:51 +0000
committerZachary Sloan2013-04-11 20:08:51 +0000
commit2b1a81ebf792d2c7d9c0bd572ebcf5bc881dfcab (patch)
treee672bea84040858b7cb8b85fe37642289ce76456 /wqflask/maintenance/generate_probesetfreeze_file.py
parent4d736528dd650793a498b24909567638972d2d08 (diff)
downloadgenenetwork2-2b1a81ebf792d2c7d9c0bd572ebcf5bc881dfcab.tar.gz
Fixed a bug with quick_search_table.py
Edited generate_probesetfreeze_file.py to try running it on the dataset with incorrect regression lines
Diffstat (limited to 'wqflask/maintenance/generate_probesetfreeze_file.py')
-rw-r--r--wqflask/maintenance/generate_probesetfreeze_file.py24
1 files changed, 12 insertions, 12 deletions
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index 95515cea..91a2b8a1 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -36,12 +36,12 @@ def get_strains(cursor):
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):
@@ -53,13 +53,13 @@ def get_probeset_vals(cursor, dataset_name):
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
@@ -73,19 +73,19 @@ def get_probeset_vals(cursor, dataset_name):
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.itervalues())[0]
+ print("\n**** first_probeset is:", pf(first_probeset))
for strain in strains:
print("\n**** strain is:", pf(strain))
- print("\n**** first_probeset is:", pf(first_probeset))
if strain in first_probeset:
trimmed_strains.append(strain)
print("trimmed_strains:", pf(trimmed_strains))
@@ -107,9 +107,9 @@ def write_data_matrix_file(strains, probeset_vals, filename):
def main():
filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
- "ProbeSetFreezeId_379_FullName_EPFL_LISP_BXD_CD_Muscle_Affy_Mouse_Gene_1.0_ST_" +
- "(Dec11)_RMA_**.txt")
- dataset_name = "EPFLMouseMuscleCDRMA1211"
+ "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
+ "(Oct08)_RankInv_Beta.txt")
+ dataset_name = "Eye_AXBXA_1008_RankInv"
cursor = get_cursor()
strains = get_strains(cursor)