diff options
Diffstat (limited to 'wqflask/maintenance/generate_probesetfreeze_file.py')
| -rw-r--r-- | wqflask/maintenance/generate_probesetfreeze_file.py | 24 |
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) |