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-rw-r--r--misc/notes.txt8
-rw-r--r--wqflask/maintenance/print_benchmark.py43
-rw-r--r--wqflask/maintenance/quick_search_table.py137
-rw-r--r--wqflask/other_config/pylintrc264
-rw-r--r--wqflask/wqflask/correlation/correlation_plot.py7
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py38
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/process_plink.py28
7 files changed, 457 insertions, 68 deletions
diff --git a/misc/notes.txt b/misc/notes.txt
index 6bdcccf3..5d4bcaeb 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -106,6 +106,14 @@ sudo /etc/init.d/redis_6379 start
===========================================
+Run pylint:
+pylint file_name
+
+For options:
+pylint --help
+
+===========================================
+
Start screen session:
If "no option -R":
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
new file mode 100644
index 00000000..540e0904
--- /dev/null
+++ b/wqflask/maintenance/print_benchmark.py
@@ -0,0 +1,43 @@
+#!/usr/bin/python
+
+from __future__ import absolute_import, print_function, division
+
+import time
+
+from pprint import pformat as pf
+
+
+class TheCounter(object):
+ Counters = {}
+
+ def __init__(self):
+ start_time = time.time()
+ for counter in range(170000):
+ self.print_it(counter)
+ self.time_took = time.time() - start_time
+ TheCounter.Counters[self.__class__.__name__] = self.time_took
+
+class PrintAll(TheCounter):
+ def print_it(self, counter):
+ print(counter)
+
+class PrintSome(TheCounter):
+ def print_it(self, counter):
+ if counter % 1000 == 0:
+ print(counter)
+
+class PrintNone(TheCounter):
+ def print_it(self, counter):
+ pass
+
+
+def new_main():
+ print("Running new_main")
+ tests = [PrintAll, PrintSome, PrintNone]
+ for test in tests:
+ test()
+
+ print(pf(TheCounter.Counters))
+
+if __name__ == '__main__':
+ new_main() \ No newline at end of file
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py
index 046a05c4..4f2cd8a9 100644
--- a/wqflask/maintenance/quick_search_table.py
+++ b/wqflask/maintenance/quick_search_table.py
@@ -1,17 +1,17 @@
-from __future__ import print_function, division, absolute_import
+"""Creates a table used for the quick search feature.
+
+One column contains the terms to match the user's search against. Another contains the result
+fields in json format
-"""
Results will be returned for each of several trait types: mRNA assays, phenotypes, genotypes, and
(maybe later) genes
-For each trait type, the results for each species should be given; for example, have a "Mouse" tab
-with the mouse traits in a table inside it
-
-This table will then list each trait, its dataset, and several columns determined by its trait type
-(phenotype, genotype, etc)
+For each trait type, the results for each species should be given This table will then list
+each trait, its dataset, and several columns determined by its trait type (phenotype, genotype, etc)
"""
+from __future__ import print_function, division, absolute_import
import sys
sys.path.append("../../..")
@@ -19,19 +19,17 @@ sys.path.append("../../..")
import simplejson as json
import sqlalchemy as sa
-from sqlalchemy.dialects import mysql
-from sqlalchemy.orm import scoped_session, sessionmaker, relationship, backref
-from sqlalchemy.orm.exc import NoResultFound
+from sqlalchemy.orm import scoped_session, sessionmaker
from sqlalchemy.ext.declarative import declarative_base
-from pprint import pformat as pf
+#from pprint import pformat as pf
import zach_settings as settings
Engine = sa.create_engine(settings.SQLALCHEMY_DATABASE_URI,
#encoding='utf-8',
#client_encoding='utf-8',
- #echo="debug",
+ #echo="debug",w
)
Session = scoped_session(sessionmaker(bind=Engine)) #, extension=VersionedListener()))
@@ -41,6 +39,14 @@ Metadata = sa.MetaData()
Metadata.bind = Engine
class PublishXRef(Base):
+ """Class that corresponds with the PublishXRef table in the database.
+
+ The PublishXRef table links phenotype traits and their publications.
+
+ This class is used to add phenotype traits to the quick search table.
+
+ """
+
__tablename__ = 'PublishXRef'
Id = sa.Column(sa.Integer, primary_key=True)
@@ -56,15 +62,16 @@ class PublishXRef(Base):
@classmethod
def run(cls):
+ """Connects to database and inserts phenotype trait info into the Quicksearch table."""
conn = Engine.connect()
counter = 0
- for ps in page_query(Session.query(cls)): #all()
+ for pub_row in page_query(Session.query(cls)): #all()
values = {}
values['table_name'] = cls.__tablename__
- values['the_key'] = json.dumps([ps.Id, ps.InbredSetId])
- values['terms'] = cls.get_unique_terms(ps.Id, ps.InbredSetId)
+ values['the_key'] = json.dumps([pub_row.Id, pub_row.InbredSetId])
+ values['terms'] = cls.get_unique_terms(pub_row.Id, pub_row.InbredSetId)
print("terms is:", values['terms'])
- values['result_fields'] = cls.get_result_fields(ps.Id, ps.InbredSetId)
+ values['result_fields'] = cls.get_result_fields(pub_row.Id, pub_row.InbredSetId)
ins = QuickSearch.insert().values(**values)
conn.execute(ins)
counter += 1
@@ -72,6 +79,7 @@ class PublishXRef(Base):
@staticmethod
def get_unique_terms(publishxref_id, inbredset_id):
+ """Finds unique terms for each item in the PublishXRef table to match a query against"""
results = Session.query(
"pre_publication_description",
"post_publication_description",
@@ -119,6 +127,7 @@ class PublishXRef(Base):
@staticmethod
def get_result_fields(publishxref_id, inbredset_id):
+ """Gets the result fields (columns) that appear on the result page as a json string"""
results = Session.query(
"phenotype_id",
"species",
@@ -136,7 +145,7 @@ class PublishXRef(Base):
"Phenotype.Original_description as description, "
"PublishXRef.LRS as lrs, "
"PublishXRef.PublicationId as publication_id, "
- "Publication.PubMed_ID"
+ "Publication.PubMed_ID as pubmed_id, "
"Publication.Year as year, "
"Publication.Authors as authors "
"FROM PublishXRef, "
@@ -150,17 +159,10 @@ class PublishXRef(Base):
"PublishXRef.PublicationId = Publication.Id and "
"InbredSet.Id = :inbredset_id and "
"Species.Id = InbredSet.SpeciesId ").params(publishxref_id=publishxref_id,
- inbredset_id=inbredset_id).all()
- #"InbredSet.SpeciesId = Species.Id and "
- #"Geno.SpeciesId = Species.Id and "
- #"Geno.Name = PublishXRef.Locus ").params(publishxref_id=publishxref_id,
- # inbredset_id=inbredset_id).all()
- #for result in results:
- # print("****", result)
+ inbredset_id=inbredset_id).all()
assert len(set(result for result in results)) == 1, "Different results or no results"
- #print("results are:", results)
result = results[0]
result = row2dict(result)
try:
@@ -176,7 +178,16 @@ class PublishXRef(Base):
return json_results
+
class GenoXRef(Base):
+ """Class that corresponds with the GenoXRef table in the database.
+
+ The GenoXRef table links genotype traits and their data.
+
+ This class is used to add genotype traits to the quick search table.
+
+ """
+
__tablename__ = 'GenoXRef'
GenoFreezeId = sa.Column(sa.Integer, primary_key=True)
@@ -187,6 +198,7 @@ class GenoXRef(Base):
@classmethod
def run(cls):
+ """Connects to database and inserts genotype trait info into the Quicksearch table."""
conn = Engine.connect()
counter = 0
for item in page_query(Session.query(cls)): #all()
@@ -201,9 +213,10 @@ class GenoXRef(Base):
conn.execute(ins)
counter += 1
print("Done:", counter)
-
+
@staticmethod
def get_unique_terms(geno_id):
+ """Finds unique terms for each item in the GenoXRef table to match a query against"""
print("geno_id: ", geno_id)
results = Session.query(
"name",
@@ -214,8 +227,6 @@ class GenoXRef(Base):
"FROM Geno "
"WHERE Geno.Id = :geno_id ").params(geno_id=geno_id).all()
- #print("results: ", pf(results))
-
unique = set()
if len(results):
for item in results[0]:
@@ -234,12 +245,12 @@ class GenoXRef(Base):
continue
unique.add(token)
- #print("\nUnique terms are: {}\n".format(unique))
return " ".join(unique)
@staticmethod
def get_result_fields(geno_id, dataset_id):
+ """Gets the result fields (columns) that appear on the result page as a json string"""
results = Session.query(
"name",
"marker_name",
@@ -271,11 +282,8 @@ class GenoXRef(Base):
"InbredSet.Id = GenoFreeze.InbredSetId and "
"InbredSet.SpeciesId = Species.Id ").params(geno_id=geno_id,
dataset_id=dataset_id).all()
- #for result in results:
- # print(result)
assert len(set(result for result in results)) == 1, "Different results"
- #print("results are:", results)
result = results[0]
result = row2dict(result)
try:
@@ -292,6 +300,14 @@ class GenoXRef(Base):
return json_results
class ProbeSetXRef(Base):
+ """Class that corresponds with the ProbeSetXRef table in the database.
+
+ The ProbeSetXRef table links mRNA expression traits and their sample data.
+
+ This class is used to add mRNA expression traits to the quick search table.
+
+ """
+
__tablename__ = 'ProbeSetXRef'
ProbeSetFreezeId = sa.Column(sa.Integer, primary_key=True)
@@ -310,16 +326,17 @@ class ProbeSetXRef(Base):
@classmethod
def run(cls):
+ """Connects to db and inserts mRNA expression trait info into the Quicksearch table."""
conn = Engine.connect()
counter = 0
- for ps in page_query(Session.query(cls)): #all()
+ for ps_row in page_query(Session.query(cls)): #all()
values = {}
values['table_name'] = cls.__tablename__
- values['the_key'] = json.dumps([ps.ProbeSetId, ps.ProbeSetFreezeId])
- values['terms'] = cls.get_unique_terms(ps.ProbeSetId)
+ values['the_key'] = json.dumps([ps_row.ProbeSetId, ps_row.ProbeSetFreezeId])
+ values['terms'] = cls.get_unique_terms(ps_row.ProbeSetId)
print("terms is:", values['terms'])
- #values['species'] = get_species("ProbeSet", ps.Id)
- values['result_fields'] = cls.get_result_fields(ps.ProbeSetId, ps.ProbeSetFreezeId)
+ values['result_fields'] = cls.get_result_fields(ps_row.ProbeSetId,
+ ps_row.ProbeSetFreezeId)
if values['result_fields'] == None:
continue
ins = QuickSearch.insert().values(**values)
@@ -329,6 +346,7 @@ class ProbeSetXRef(Base):
@staticmethod
def get_unique_terms(probeset_id):
+ """Finds unique terms for each item in the ProbeSetXRef table to match a query against"""
results = Session.query(
"name",
"symbol",
@@ -345,7 +363,6 @@ class ProbeSetXRef(Base):
unique = set()
if len(results):
for item in results[0]:
- #print("locals:", locals())
if not item:
continue
for token in item.split():
@@ -366,12 +383,12 @@ class ProbeSetXRef(Base):
continue
unique.add(token)
- #print("\nUnique terms are: {}\n".format(unique))
return " ".join(unique)
@staticmethod
def get_result_fields(probeset_id, dataset_id):
+ """Gets the result fields (columns) that appear on the result page as a json string"""
print("probeset_id: ", probeset_id)
print("dataset_id: ", dataset_id)
results = Session.query(
@@ -420,14 +437,10 @@ class ProbeSetXRef(Base):
"ProbeFreeze.InbredSetId = InbredSet.Id and "
"InbredSet.SpeciesId = Species.Id ").params(probeset_id=probeset_id,
dataset_id=dataset_id).all()
- #for result in results:
- # print("-", result)
if len(set(result for result in results)) != 1:
return None
- #assert len(set(result for result in results)) == 1, "Different results"
-
- #print("results are:", results)
+
result = results[0]
result = row2dict(result)
try:
@@ -443,41 +456,47 @@ class ProbeSetXRef(Base):
return json_results
-
QuickSearch = sa.Table("QuickSearch", Metadata,
+ # table_name is the table that item is inserted from
sa.Column('table_name', sa.String(15),
- primary_key=True, nullable=False, autoincrement=False), # table that item is inserted from
+ primary_key=True, nullable=False, autoincrement=False),
sa.Column('the_key', sa.String(30),
primary_key=True, nullable=False, autoincrement=False), # key in database table
sa.Column('terms', sa.Text), # terms to compare search string with
- sa.Column('result_fields', sa.Text) # json
+ sa.Column('result_fields', sa.Text), # json
+ mysql_engine = 'MyISAM',
)
-QuickSearch.drop(Engine, checkfirst=True)
-Metadata.create_all(Engine)
+#QuickSearch.drop(Engine, checkfirst=True)
+#Metadata.create_all(Engine)
def row2dict(row):
- """http://stackoverflow.com/a/2848519/1175849"""
+ """From http://stackoverflow.com/a/2848519/1175849"""
return dict(zip(row.keys(), row))
-def page_query(q):
- """http://stackoverflow.com/a/1217947/1175849"""
+def page_query(query):
+ """From http://stackoverflow.com/a/1217947/1175849"""
offset = 0
while True:
- r = False
- for elem in q.limit(1000).offset(offset):
- r = True
- yield elem
+ rrr = False
+ for elem in query.limit(1000).offset(offset):
+ rrr = True
+ yield elem
offset += 1000
- if not r:
+ if not rrr:
break
def main():
- ProbeSetXRef.run()
- GenoXRef.run()
+ """Populate the QuickSearch table that is used with the quick search features.
+
+ Add all items from the ProbeSetXRef, GenoXRef, and PublishXRef tables to the QuickSearch tables.
+
+ """
+ #ProbeSetXRef.run()
+ #GenoXRef.run()
PublishXRef.run()
if __name__ == "__main__":
diff --git a/wqflask/other_config/pylintrc b/wqflask/other_config/pylintrc
new file mode 100644
index 00000000..b23af7a4
--- /dev/null
+++ b/wqflask/other_config/pylintrc
@@ -0,0 +1,264 @@
+[MASTER]
+
+# Specify a configuration file.
+#rcfile=
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+#init-hook=
+
+# Profiled execution.
+profile=no
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=
+
+
+[MESSAGES CONTROL]
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time. See also the "--disable" option for examples.
+#enable=
+
+# Disable the message, report, category or checker with the given id(s). You
+# can either give multiple identifiers separated by comma (,) or put this
+# option multiple times (only on the command line, not in the configuration
+# file where it should appear only once).You can also use "--disable=all" to
+# disable everything first and then reenable specific checks. For example, if
+# you want to run only the similarities checker, you can use "--disable=all
+# --enable=similarities". If you want to run only the classes checker, but have
+# no Warning level messages displayed, use"--disable=all --enable=classes
+# --disable=W"
+disable=no-init, star-args, no-member, import-error
+
+
+[REPORTS]
+
+# Set the output format. Available formats are text, parseable, colorized, msvs
+# (visual studio) and html. You can also give a reporter class, eg
+# mypackage.mymodule.MyReporterClass.
+output-format=text
+
+# Include message's id in output
+include-ids=no
+
+# Include symbolic ids of messages in output
+symbols=no
+
+# Put messages in a separate file for each module / package specified on the
+# command line instead of printing them on stdout. Reports (if any) will be
+# written in a file name "pylint_global.[txt|html]".
+files-output=no
+
+# Tells whether to display a full report or only the messages
+reports=yes
+
+# Python expression which should return a note less than 10 (10 is the highest
+# note). You have access to the variables errors warning, statement which
+# respectively contain the number of errors / warnings messages and the total
+# number of statements analyzed. This is used by the global evaluation report
+# (RP0004).
+evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10)
+
+# Add a comment according to your evaluation note. This is used by the global
+# evaluation report (RP0004).
+comment=no
+
+
+[SIMILARITIES]
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+ignore-imports=no
+
+
+[VARIABLES]
+
+# Tells whether we should check for unused import in __init__ files.
+init-import=no
+
+# A regular expression matching the beginning of the name of dummy variables
+# (i.e. not used).
+dummy-variables-rgx=_|dummy
+
+# List of additional names supposed to be defined in builtins. Remember that
+# you should avoid to define new builtins when possible.
+additional-builtins=
+
+
+[BASIC]
+
+# Required attributes for module, separated by a comma
+required-attributes=
+
+# List of builtins function names that should not be used, separated by a comma
+bad-functions=map,filter,apply,input
+
+# Regular expression which should only match correct module names
+module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Regular expression which should only match correct module level names
+const-rgx=(([A-Z_][A-Za-z0-9_]*)|(__.*__))$
+
+# Regular expression which should only match correct class names
+class-rgx=[A-Z_][a-zA-Z0-9]+$
+
+# Regular expression which should only match correct function names
+function-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct method names
+method-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct instance attribute names
+attr-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct argument names
+argument-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct variable names
+variable-rgx=[a-z_][a-z0-9_]{2,30}$
+
+# Regular expression which should only match correct list comprehension /
+# generator expression variable names
+inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
+
+# Good variable names which should always be accepted, separated by a comma
+good-names=i,j,k,ex,Run,_
+
+# Bad variable names which should always be refused, separated by a comma
+bad-names=foo,bar,baz,toto,tutu,tata
+
+# Regular expression which should only match functions or classes name which do
+# not require a docstring
+no-docstring-rgx=__.*__
+
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+max-line-length=100
+
+# Maximum number of lines in a module
+max-module-lines=1000
+
+# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1
+# tab).
+indent-string=' '
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,XXX,TODO
+
+
+[TYPECHECK]
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# mixin class is detected if its name ends with "mixin" (case insensitive).
+ignore-mixin-members=yes
+
+# List of classes names for which member attributes should not be checked
+# (useful for classes with attributes dynamically set).
+ignored-classes=SQLObject
+
+# When zope mode is activated, add a predefined set of Zope acquired attributes
+# to generated-members.
+zope=no
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E0201 when accessed. Python regular
+# expressions are accepted.
+generated-members=REQUEST,acl_users,aq_parent
+
+
+[DESIGN]
+
+# Maximum number of arguments for function / method
+max-args=5
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names=_.*
+
+# Maximum number of locals for function / method body
+max-locals=15
+
+# Maximum number of return / yield for function / method body
+max-returns=6
+
+# Maximum number of branch for function / method body
+max-branchs=12
+
+# Maximum number of statements in function / method body
+max-statements=50
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=2
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=20
+
+
+[IMPORTS]
+
+# Deprecated modules which should not be used, separated by a comma
+deprecated-modules=regsub,string,TERMIOS,Bastion,rexec
+
+# Create a graph of every (i.e. internal and external) dependencies in the
+# given file (report RP0402 must not be disabled)
+import-graph=
+
+# Create a graph of external dependencies in the given file (report RP0402 must
+# not be disabled)
+ext-import-graph=
+
+# Create a graph of internal dependencies in the given file (report RP0402 must
+# not be disabled)
+int-import-graph=
+
+
+[CLASSES]
+
+# List of interface methods to ignore, separated by a comma. This is used for
+# instance to not check methods defines in Zope's Interface base class.
+ignore-iface-methods=isImplementedBy,deferred,extends,names,namesAndDescriptions,queryDescriptionFor,getBases,getDescriptionFor,getDoc,getName,getTaggedValue,getTaggedValueTags,isEqualOrExtendedBy,setTaggedValue,isImplementedByInstancesOf,adaptWith,is_implemented_by
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,__new__,setUp
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg=cls
+
+# List of valid names for the first argument in a metaclass class method.
+valid-metaclass-classmethod-first-arg=mcs
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception"
+overgeneral-exceptions=Exception
diff --git a/wqflask/wqflask/correlation/correlation_plot.py b/wqflask/wqflask/correlation/correlation_plot.py
index 4b043fc3..c2b64d70 100644
--- a/wqflask/wqflask/correlation/correlation_plot.py
+++ b/wqflask/wqflask/correlation/correlation_plot.py
@@ -24,6 +24,10 @@ class CorrelationPlot(object):
self.samples_1 = self.get_samples(self.dataset1, sample_names_1, self.trait1)
self.samples_2 = self.get_samples(self.dataset2, sample_names_2, self.trait2)
+ coords = {}
+ for sample in self.samples_1:
+ coords[sample.name] = (sample.val)
+
def get_sample_names(self, dataset):
if dataset.group.parlist:
@@ -45,4 +49,5 @@ class CorrelationPlot(object):
sample_group_type='primary',
header="%s Only" % (dataset.group.name))
- return samples \ No newline at end of file
+ return samples
+ \ No newline at end of file
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index a3ba8fdb..10221a2e 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -28,6 +28,7 @@ from scipy import stats
import pdb
import gzip
+import datetime
import cPickle as pickle
import simplejson as json
@@ -38,6 +39,9 @@ from utility import temp_data
from wqflask.my_pylmm.pyLMM import chunks
+import redis
+Redis = redis.Redis()
+
#np.seterr('raise')
def run_human(pheno_vector,
@@ -65,6 +69,7 @@ def run_human(pheno_vector,
covariate_matrix)
lmm_ob.fit()
+
# Buffers for pvalues and t-stats
p_values = []
t_stats = []
@@ -86,19 +91,36 @@ def run_human(pheno_vector,
with Bench("Create list of inputs"):
inputs = list(plink_input)
-
+
with Bench("Divide into chunks"):
results = chunks.divide_into_chunks(inputs, 64)
result_store = []
- identifier = uuid.uuid4()
- for part, result in enumerate(results):
- # todo: Don't use TempData here. Instead revert old one and store this stuff as a list
- data_store = temp_data.TempData(identifier, "plink", part)
-
- data_store.store("data", pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
- result_store.append(data_store)
+ identifier = str(uuid.uuid4())
+
+ lmm_vars = pickle.dumps(dict(
+ pheno_vector = pheno_vector,
+ covariate_matrix = covariate_matrix,
+ kinship_matrix = kinship_matrix
+ ))
+ Redis.hset(identifier, "lmm_vars", pickle.dumps(lmm_vars))
+
+ key = "plink_inputs"
+ timestamp = datetime.datetime.utcnow().isoformat()
+
+ for part, result in enumerate(results):
+ #data = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+ holder = pickle.dumps(dict(
+ identifier = identifier,
+ part = part,
+ timestamp = timestamp,
+ result = result
+ ), pickle.HIGHEST_PROTOCOL)
+ print("Adding:", part)
+ Redis.rpush(key, holder)
+
+ print("***** Added to {} queue *****".format(key))
for snp, this_id in plink_input:
with Bench("part before association"):
if count > 2000:
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py b/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
new file mode 100644
index 00000000..1274fe50
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
@@ -0,0 +1,28 @@
+from __future__ import absolute_import, print_function, division
+
+import cPickle as pickle
+import redis
+Redis = redis.Redis()
+
+from wqflask.my_pylmm.pyLMM import lmm
+
+lmm_vars_pickled = Redis.get("lmm_vars")
+
+
+plink_pickled = Redis.lpop("plink_inputs")
+
+plink_data = pickle.loads(plink_pickled)
+
+identifier = plink_data['identifier']
+print("identifier: ", identifier)
+
+
+
+ps, ts = lmm.human_association(snp,
+ n,
+ keep,
+ lmm_ob,
+ pheno_vector,
+ covariate_matrix,
+ kinship_matrix,
+ refit)