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| author | zsloan | 2021-05-06 18:07:19 -0500 |
|---|---|---|
| committer | GitHub | 2021-05-06 18:07:19 -0500 |
| commit | 9ed3c226c561d80957e34294f884fe48373cf6e6 (patch) | |
| tree | 7b3c603b961aa4b840d82ef289887b0a31c0f676 /wqflask/maintenance/generate_probesetfreeze_file.py | |
| parent | 2444d60a93ef7c9900ed9a52877bff0ee08fbfb6 (diff) | |
| parent | 3c430082b767a29c3e35cb03e68c1b22373ad353 (diff) | |
| download | genenetwork2-9ed3c226c561d80957e34294f884fe48373cf6e6.tar.gz | |
Merge branch 'testing' into bug/fix_rqtl_covariates
Diffstat (limited to 'wqflask/maintenance/generate_probesetfreeze_file.py')
| -rw-r--r-- | wqflask/maintenance/generate_probesetfreeze_file.py | 14 |
1 files changed, 11 insertions, 3 deletions
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py index b1e41e9a..e964c8ed 100644 --- a/wqflask/maintenance/generate_probesetfreeze_file.py +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -23,10 +23,12 @@ def get_cursor(): cursor = con.cursor() return cursor + 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 @@ -42,6 +44,7 @@ def get_strains(cursor): return strains + def get_probeset_vals(cursor, dataset_name): cursor.execute(""" select ProbeSet.Id, ProbeSet.Name from ProbeSetXRef, @@ -77,6 +80,7 @@ def get_probeset_vals(cursor, dataset_name): return probeset_vals + def trim_strains(strains, probeset_vals): trimmed_strains = [] #print("probeset_vals is:", pf(probeset_vals)) @@ -89,6 +93,7 @@ def trim_strains(strains, probeset_vals): 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) @@ -103,10 +108,12 @@ def write_data_matrix_file(strains, probeset_vals, filename): 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") + 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" cursor = get_cursor() @@ -117,5 +124,6 @@ def main(): trimmed_strains = trim_strains(strains, probeset_vals) write_data_matrix_file(trimmed_strains, probeset_vals, filename) + if __name__ == '__main__': main() |