Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 101 deletions

diff --git a/web/webqtl/snpBrowser/snpDetails.py b/web/webqtl/snpBrowser/snpDetails.py
deleted file mode 100755
index 43100ba9..00000000
--- a/web/webqtl/snpBrowser/snpDetails.py
+++ /dev/null
@@ -1,101 +0,0 @@
-# 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