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authorBonfaceKilz2020-08-26 19:12:33 +0300
committerBonfaceKilz2020-08-26 19:12:33 +0300
commit303e4b71c2172da5be19c84d4be5a062329ac013 (patch)
tree130496e7b4c6fe2157c14abd50be941823ed40b9 /wqflask/maintenance
parent7717f0d3d4802d115a8b5ace4d379864ba5b1188 (diff)
downloadgenenetwork2-303e4b71c2172da5be19c84d4be5a062329ac013.tar.gz
Remove "from __future__ import new_feature" statements
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/convert_dryad_to_bimbam.py3
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py3
-rw-r--r--wqflask/maintenance/gen_select_dataset.py10
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py3
-rw-r--r--wqflask/maintenance/generate_probesetfreeze_file.py2
-rw-r--r--wqflask/maintenance/geno_to_json.py3
-rw-r--r--wqflask/maintenance/get_group_samplelists.py2
-rw-r--r--wqflask/maintenance/print_benchmark.py4
-rw-r--r--wqflask/maintenance/quantile_normalize.py7
-rw-r--r--wqflask/maintenance/set_resource_defaults.py4
10 files changed, 8 insertions, 33 deletions
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index e833b395..12ce35e9 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -6,7 +6,6 @@ Convert data dryad files to a BIMBAM _geno and _snps file
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
@@ -67,4 +66,4 @@ def convert_dryad_to_bimbam(filename):
if __name__=="__main__":
input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
- convert_dryad_to_bimbam(input_filename) \ No newline at end of file
+ convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 528b98cf..d49742f2 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -9,7 +9,6 @@ code
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
import os
@@ -187,4 +186,4 @@ if __name__=="__main__":
#convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
#convertob.convert()
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
- #ConvertGenoFiles(Geno_Directory) \ No newline at end of file
+ #ConvertGenoFiles(Geno_Directory)
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index fd65a52a..544e2fd1 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -30,14 +30,6 @@ It needs to be run manually when database has been changed. Run it as
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-from __future__ import print_function, division
-
-#from flask import config
-#
-#cdict = {}
-#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS')
-#print("cdict is:", cdict)
-
import sys
# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
@@ -319,4 +311,4 @@ def _test_it():
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
- main() \ No newline at end of file
+ main()
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index b53f5dda..60257b28 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -8,7 +8,6 @@ and uses GEMMA to generate their corresponding kinship/relatedness matrix file
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
import os
@@ -58,4 +57,4 @@ if __name__=="__main__":
Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
- #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file
+ #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index 4231cc7c..b1e41e9a 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -1,7 +1,5 @@
#!/usr/bin/python
-from __future__ import absolute_import, print_function, division
-
import sys
# sys.path.insert(0, "..") - why?
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 9579812a..7e7fd241 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -9,7 +9,6 @@ code
"""
-from __future__ import print_function, division, absolute_import
import sys
sys.path.append("..")
import os
@@ -194,4 +193,4 @@ if __name__=="__main__":
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
#ConvertGenoFiles(Geno_Directory)
- #process_csv(Input_File, Output_File) \ No newline at end of file
+ #process_csv(Input_File, Output_File)
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index fb22898a..3f9d0278 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
import os
import glob
import gzip
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index ae327cf3..b24ce4f1 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -1,7 +1,5 @@
#!/usr/bin/python
-from __future__ import absolute_import, print_function, division
-
import time
from pprint import pformat as pf
@@ -40,4 +38,4 @@ def new_main():
print(pf(TheCounter.Counters))
if __name__ == '__main__':
- new_main() \ No newline at end of file
+ new_main()
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 4d6e03bf..701b2b50 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -1,10 +1,5 @@
-from __future__ import absolute_import, print_function, division
-
import sys
sys.path.insert(0, './')
-
-
-
import MySQLdb
import urllib.parse
@@ -126,4 +121,4 @@ if __name__ == '__main__':
}
)
- print(response) \ No newline at end of file
+ print(response)
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index abd5416c..4177c124 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -16,8 +16,6 @@ To run:
"""
-from __future__ import print_function, division
-
import sys
import json
@@ -163,4 +161,4 @@ def main():
if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
- main() \ No newline at end of file
+ main()