Add all the source codes into the github.

1 files changed, 101 insertions, 0 deletions

diff --git a/web/webqtl/snpBrowser/snpDetails.py b/web/webqtl/snpBrowser/snpDetails.py
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+++ 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']
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