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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
#########################################
# A class for the information of SNPs ONLY. This is for the 'extra' page when you click on a SNP that doesn't have an RS#
# This is where the information populating
# The table is gathered. This is where you determine what variables you will display in the table
#########################################
import string
from htmlgen import HTMLgen2 as HT
import snpBrowserUtils
from base.templatePage import templatePage
from snpBrowserPage import snpBrowserPage
class snpDetails(templatePage):
def __init__(self, fd, snpId):
templatePage.__init__(self, fd)
snpCols = "snpname, chromosome, mb, domain, rs, function, type, majorAllele, majorCount, minorAllele, minorCount, class, flanking5, flanking3, blatScore, sourceId, gene, ncbi".split(", ")
#get the details from the database if search the SNP variants by the "gene/snp" field
if snpId:
self.openMysql()
mysqlField = ['snpname','rs', 'chromosome', 'mb', 'function', 'type', 'class', 'flanking5', 'flanking3', 'blatscore', 'domain', 'gene', 'ncbi']
query = """
SELECT
%s, c.Name,b.*
from
SnpAll a, SnpPattern b, SnpSource c
where
a.Id =%s AND a.Id = b.SnpId AND a.SourceId =c.Id
""" % (string.join(mysqlField, ", "), snpId)
self.cursor.execute(query)
results = self.cursor.fetchone()
result =results[:14]
mysqlField.append('sourceName')
snpDict = {}
for i, item in enumerate(result):
snpDict[mysqlField[i]] = item
alleleList =results[15:]
objSnpBrowserPage =snpBrowserPage(fd)
flag =0
majAllele,minAllele,majAlleleCount,minAlleleCount= objSnpBrowserPage.getMajMinAlleles(alleleList,flag)
snpDict['majorAllele'] = majAllele
snpDict['minorAllele'] = minAllele
snpDict['majorCount'] = majAlleleCount
snpDict['minorCount'] = minAlleleCount
else:
return
# Creates the table for the SNP data
snpTable = HT.TableLite(border=0, cellspacing=5, cellpadding=3, Class="collap")
for item in snpCols:
thisTR = HT.TR(HT.TD(snpBrowserUtils.columnNames[item], Class="fs14 fwb ffl b1 cw cbrb", NOWRAP = 1))
if item in ('flanking5', 'flanking3'):
seq0 = snpDict[item]
seq = ""
i = 0
if seq0:
while i < len(seq0):
seq += seq0[i:i+5] + " "
i += 5
thisTR.append(HT.TD(HT.Span(seq, Class="code", Id="green"), Class='fs13 b1 cbw c222'))
elif item in snpDict.keys() and snpDict[item]:
thisTR.append(HT.TD(snpDict[item], Class='fs13 b1 cbw c222'))
else:
thisTR.append(HT.TD("", Class='fs13 b1 cbw c222'))
snpTable.append(thisTR)
self.dict['body'] = HT.TD(HT.Paragraph("Details for %s" % snpDict['snpname'], Class="title"), HT.Blockquote(snpTable))
self.dict['title'] = "Details for %s" % snpDict['snpname']
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