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-rw-r--r--wqflask/base/data_set.py200
1 files changed, 123 insertions, 77 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index fddfce58..54dd3c4b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -44,7 +44,7 @@ from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility.benchmark import Bench
from utility import chunks
-from utility.tools import locate, locate_ignore_error
+from utility.tools import locate, locate_ignore_error, flat_files
from maintenance import get_group_samplelists
@@ -53,7 +53,7 @@ from pprint import pformat as pf
from db.gn_server import menu_main
from db.call import fetchall,fetchone,fetch1
-from utility.tools import USE_GN_SERVER, USE_REDIS
+from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -226,7 +226,7 @@ class Markers(object):
class HumanMarkers(Markers):
def __init__(self, name, specified_markers = []):
- marker_data_fh = open(locate('genotype') + '/' + name + '.bim')
+ marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
@@ -264,96 +264,74 @@ class DatasetGroup(object):
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
#logger.debug("DATASET NAME2:", dataset.name)
- self.name, self.id = fetchone(dataset.query_for_group)
+ self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
- #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list))
+
+ self.accession_id = self.get_accession_id()
+ self.mapping_id, self.mapping_names = self.get_mapping_methods()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
self.allsamples = None
self._datasets = None
+ self.genofile = None
+
+ def get_accession_id(self):
+ results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
+ InbredSet.Name = %s and
+ PublishFreeze.InbredSetId = InbredSet.Id and
+ InfoFiles.InfoPageName = PublishFreeze.Name and
+ PublishFreeze.public > 0 and
+ PublishFreeze.confidentiality < 1 order by
+ PublishFreeze.CreateTime desc""", (self.name)).fetchone()
+
+ if results != None:
+ return str(results[0])
+ else:
+ return "None"
+
+ def get_mapping_methods(self):
+
+ mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
+ if mapping_id == "1":
+ mapping_names = ["QTLReaper", "PYLMM", "R/qtl"]
+ elif mapping_id == "2":
+ mapping_names = ["GEMMA"]
+ elif mapping_id == "4":
+ mapping_names = ["PLINK"]
+ else:
+ mapping_names = []
+
+ return mapping_id, mapping_names
def get_specified_markers(self, markers = []):
self.markers = HumanMarkers(self.name, markers)
def get_markers(self):
- #logger.debug("self.species is:", self.species)
- if self.species == "human":
+ logger.debug("self.species is:", self.species)
+
+ def check_plink_gemma():
+ if flat_file_exists("mapping"):
+ MAPPING_PATH = flat_files("mapping")+"/"
+ if (os.path.isfile(MAPPING_PATH+self.name+".bed") and
+ (os.path.isfile(MAPPING_PATH+self.name+".map") or
+ os.path.isfile(MAPPING_PATH+self.name+".bim"))):
+ return True
+ return False
+
+ if check_plink_gemma():
marker_class = HumanMarkers
else:
- marker_class = Markers
+ marker_class = Markers
self.markers = marker_class(self.name)
- def datasets(self):
- key = "group_dataset_menu:v2:" + self.name
- logger.debug("key is2:", key)
- dataset_menu = []
- logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
- logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
- the_results = fetchall('''
- (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
- FROM PublishFreeze,InbredSet
- WHERE PublishFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = '%s'
- and PublishFreeze.public > %s)
- UNION
- (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
- FROM GenoFreeze, InbredSet
- WHERE GenoFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = '%s'
- and GenoFreeze.public > %s)
- UNION
- (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
- FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
- WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
- and ProbeFreeze.TissueId = Tissue.Id
- and ProbeFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name like %s
- and ProbeSetFreeze.public > %s
- ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
- ''' % (self.name, webqtlConfig.PUBLICTHRESH,
- self.name, webqtlConfig.PUBLICTHRESH,
- "'" + self.name + "'", webqtlConfig.PUBLICTHRESH))
-
- #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
- for dataset_item in the_results:
- tissue_name = dataset_item[0]
- dataset = dataset_item[1]
- dataset_short = dataset_item[2]
- if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
- dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
- else:
- dataset_sub_menu = [item[1:] for item in dataset]
-
- tissue_already_exists = False
- tissue_position = None
- for i, tissue_dict in enumerate(dataset_menu):
- if tissue_dict['tissue'] == tissue_name:
- tissue_already_exists = True
- tissue_position = i
- break
-
- if tissue_already_exists:
- #logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
- dataset_menu[i]['datasets'].append((dataset, dataset_short))
- else:
- dataset_menu.append(dict(tissue=tissue_name,
- datasets=[(dataset, dataset_short)]))
-
- if USE_REDIS:
- Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*5)
- self._datasets = dataset_menu
-
- return self._datasets
-
def get_f1_parent_strains(self):
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
@@ -408,7 +386,10 @@ class DatasetGroup(object):
genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
- full_filename = str(locate(self.name+'.geno','genotype'))
+ if self.genofile:
+ full_filename = str(locate(self.genofile, 'genotype'))
+ else:
+ full_filename = str(locate(self.name + '.geno', 'genotype'))
genotype_1.read(full_filename)
if genotype_1.type == "group" and self.parlist:
@@ -427,6 +408,71 @@ class DatasetGroup(object):
return genotype
+def datasets(group_name, this_group = None):
+ key = "group_dataset_menu:v2:" + group_name
+ logger.debug("key is2:", key)
+ dataset_menu = []
+ logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
+ logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
+ the_results = fetchall('''
+ (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
+ FROM PublishFreeze,InbredSet
+ WHERE PublishFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name = '%s'
+ and PublishFreeze.public > %s)
+ UNION
+ (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
+ FROM GenoFreeze, InbredSet
+ WHERE GenoFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name = '%s'
+ and GenoFreeze.public > %s)
+ UNION
+ (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
+ FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
+ WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+ and ProbeFreeze.TissueId = Tissue.Id
+ and ProbeFreeze.InbredSetId = InbredSet.Id
+ and InbredSet.Name like %s
+ and ProbeSetFreeze.public > %s
+ ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
+ ''' % (group_name, webqtlConfig.PUBLICTHRESH,
+ group_name, webqtlConfig.PUBLICTHRESH,
+ "'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
+
+ #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
+ for dataset_item in the_results:
+ tissue_name = dataset_item[0]
+ dataset = dataset_item[1]
+ dataset_short = dataset_item[2]
+ if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
+ dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ else:
+ dataset_sub_menu = [item[1:] for item in dataset]
+
+ tissue_already_exists = False
+ tissue_position = None
+ for i, tissue_dict in enumerate(dataset_menu):
+ if tissue_dict['tissue'] == tissue_name:
+ tissue_already_exists = True
+ tissue_position = i
+ break
+
+ if tissue_already_exists:
+ #logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
+ dataset_menu[i]['datasets'].append((dataset, dataset_short))
+ else:
+ dataset_menu.append(dict(tissue=tissue_name,
+ datasets=[(dataset, dataset_short)]))
+
+ if USE_REDIS:
+ Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
+ Redis.expire(key, 60*5)
+
+ if this_group != None:
+ this_group._datasets = dataset_menu
+ return this_group._datasets
+ else:
+ return dataset_menu
class DataSet(object):
"""
@@ -650,7 +696,7 @@ class PhenotypeDataSet(DataSet):
self.query_for_group = '''
SELECT
- InbredSet.Name, InbredSet.Id
+ InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
InbredSet, PublishFreeze
WHERE
@@ -720,8 +766,8 @@ class PhenotypeDataSet(DataSet):
if this_trait.lrs:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
- where Species.Name = %s and
- Geno.Name = %s and
+ where Species.Name = '%s' and
+ Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
logger.sql(query)
@@ -793,7 +839,7 @@ class GenotypeDataSet(DataSet):
self.query_for_group = '''
SELECT
- InbredSet.Name, InbredSet.Id
+ InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
InbredSet, GenoFreeze
WHERE
@@ -919,7 +965,7 @@ class MrnaAssayDataSet(DataSet):
self.query_for_group = '''
SELECT
- InbredSet.Name, InbredSet.Id
+ InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
InbredSet, ProbeSetFreeze, ProbeFreeze
WHERE
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 06:35:43 +0000