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diff --git a/web/webqtl/snpBrowser/snpDetails.py b/web/webqtl/snpBrowser/snpDetails.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
-
-#########################################
-# 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'] \ No newline at end of file