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Diffstat (limited to 'web/webqtl/snpBrowser/snpDetails.py')
| -rwxr-xr-x | web/webqtl/snpBrowser/snpDetails.py | 101 |
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']
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