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authorZachary Sloan2012-11-27 14:44:14 -0600
committerZachary Sloan2012-11-27 14:44:14 -0600
commit0931212bc692177cfc0ebcf016bc869dd4f88fd8 (patch)
treef238113134c33ab87d9fa7eafa104c8f32981878 /wqflask/base/data_set.py
parent1749c660a7e71f10bbdec04f8bf7bb77df3f3eef (diff)
downloadgenenetwork2-0931212bc692177cfc0ebcf016bc869dd4f88fd8.tar.gz
Renamed webqtlDataSet.py to data_set.py
Renamed the class webqtlDataset to DataSet Finished cisLRS and transLRS search types in d_search.py Fixed parent/f1 issue in show_trait.py
Diffstat (limited to 'wqflask/base/data_set.py')
-rwxr-xr-xwqflask/base/data_set.py162
1 files changed, 162 insertions, 0 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
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+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# Last updated by GeneNetwork Core Team 2010/10/20
+
+from htmlgen import HTMLgen2 as HT
+
+import webqtlConfig
+
+
+
+class DataSet(object):
+ """
+ Dataset class defines a dataset in webqtl, can be either Microarray,
+ Published phenotype, genotype, or user input dataset(temp)
+
+ """
+
+ def __init__(self, dbName, cursor=None):
+
+ assert dbName
+ self.id = 0
+ self.name = ''
+ self.type = ''
+ self.group = ''
+ self.cursor = cursor
+
+ #temporary storage
+ if dbName.find('Temp') >= 0:
+ self.searchfield = ['name','description']
+ self.disfield = ['name','description']
+ self.type = 'Temp'
+ self.id = 1
+ self.fullname = 'Temporary Storage'
+ self.shortname = 'Temp'
+ elif dbName.find('Publish') >= 0:
+ pass
+ elif dbName.find('Geno') >= 0:
+ self.searchfield = ['name','chr']
+ self.disfield = ['name','chr','mb', 'source2', 'sequence']
+ self.type = 'Geno'
+ else: #ProbeSet
+ self.searchfield = ['name','description','probe_target_description',
+ 'symbol','alias','genbankid','unigeneid','omim',
+ 'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score']
+ self.disfield = ['name','symbol','description','probe_target_description',
+ 'chr','mb','alias','geneid','genbankid', 'unigeneid', 'omim',
+ 'refseq_transcriptid','blatseq','targetseq','chipid', 'comments',
+ 'strand_probe','strand_gene','probe_set_target_region',
+ 'probe_set_specificity', 'probe_set_blat_score','probe_set_blat_mb_start',
+ 'probe_set_blat_mb_end', 'probe_set_strand',
+ 'probe_set_note_by_rw', 'flag']
+ self.type = 'ProbeSet'
+ self.name = dbName
+ if self.cursor and self.id == 0:
+ self.retrieveName()
+
+
+ # Delete this eventually
+ @property
+ def riset():
+ Weve_Renamed_This_As_Group
+
+
+ def get_group(self):
+ assert self.cursor
+ if self.type == 'Publish':
+ query = '''
+ SELECT
+ InbredSet.Name, InbredSet.Id
+ FROM
+ InbredSet, PublishFreeze
+ WHERE
+ PublishFreeze.InbredSetId = InbredSet.Id AND
+ PublishFreeze.Name = "%s"
+ ''' % self.name
+ elif self.type == 'Geno':
+ query = '''
+ SELECT
+ InbredSet.Name, InbredSet.Id
+ FROM
+ InbredSet, GenoFreeze
+ WHERE
+ GenoFreeze.InbredSetId = InbredSet.Id AND
+ GenoFreeze.Name = "%s"
+ ''' % self.name
+ elif self.type == 'ProbeSet':
+ query = '''
+ SELECT
+ InbredSet.Name, InbredSet.Id
+ FROM
+ InbredSet, ProbeSetFreeze, ProbeFreeze
+ WHERE
+ ProbeFreeze.InbredSetId = InbredSet.Id AND
+ ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
+ ProbeSetFreeze.Name = "%s"
+ ''' % self.name
+ else:
+ return ""
+ self.cursor.execute(query)
+ group, RIID = self.cursor.fetchone()
+ if group == 'BXD300':
+ group = "BXD"
+ self.group = group
+ self.group_id = RIID
+ return group
+
+
+ def retrieveName(self):
+ assert self.id == 0 and self.cursor
+ query = '''
+ SELECT
+ Id, Name, FullName, ShortName
+ FROM
+ %sFreeze
+ WHERE
+ public > %d AND
+ (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
+ '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name)
+ try:
+ self.cursor.execute(query)
+ self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone()
+ except:
+ raise KeyError, `self.name`+' doesn\'t exist.'
+
+
+ def genHTML(self, Class='c0dd'):
+ return HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class),
+ url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank")
+
+class PhenotypeDataSet(DataSet):
+
+ def __init__(self):
+ self.searchfield = ['name','post_publication_description','abstract','title','authors']
+ self.disfield = ['name','pubmed_id',
+ 'pre_publication_description', 'post_publication_description', 'original_description',
+ 'pre_publication_abbreviation', 'post_publication_abbreviation',
+ 'lab_code', 'submitter', 'owner', 'authorized_users',
+ 'authors','title','abstract', 'journal','volume','pages','month',
+ 'year','sequence', 'units', 'comments']
+ self.type = 'Publish' \ No newline at end of file