From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 27 Mar 2015 20:28:51 +0000
Subject: Removed everything from 'web' directory except genofiles and renamed
 the directory to 'genotype_files'

---
 web/webqtl/textUI/cmdGeno.py | 118 -------------------------------------------
 1 file changed, 118 deletions(-)
 delete mode 100755 web/webqtl/textUI/cmdGeno.py

(limited to 'web/webqtl/textUI/cmdGeno.py')

diff --git a/web/webqtl/textUI/cmdGeno.py b/web/webqtl/textUI/cmdGeno.py
deleted file mode 100755
index 8dd0f924..00000000
--- a/web/webqtl/textUI/cmdGeno.py
+++ /dev/null
@@ -1,118 +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
-
-import string
-import os
-
-import reaper
-
-from base import webqtlConfig
-from cmdClass import cmdClass
-
-#########################################
-#      Geno Class
-#########################################
-class cmdGeno(cmdClass):
-
-	def __init__(self,fd=None):
-
-		cmdClass.__init__(self,fd)
-
-		if not webqtlConfig.TEXTUI:
-			self.contents.append("Please send your request to http://robot.genenetwork.org")
-			return
-
-		if self.accessError:
-			return
-		self.error = 0
-		self.RISet = None
-		self.chr = None
-		self.dataset = None
-		self.strainList = []
-		try:
-			self.RISet = self.data.getvalue('riset')
-			if not self.RISet:
-				raise ValueError
-		except:
-			self.error = 1
-			self.contents.append('###Example : http://www.genenetwork.org%s%s?cmd=%s&riset=BXD&chr=1' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID))
-			return
-		try:
-			self.format = self.data.getvalue('format')[:3]
-		except:
-			self.format = 'row'
-
-		try:
-			self.dataset = reaper.Dataset()
-			try:
-				self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
-			except:
-				self.dataset.read(os.path.join(webqtlConfig.GENODIR, self.RISet.upper() + '.geno'))
-			self.strainList = list(self.dataset.prgy)
-		except:
-			self.error = 1
-			#traceback.print_exc()	
-			self.contents.append('###The name of RISet is incorrect')
-			return
-
-		try:
-			self.chr = self.data.getvalue('chr')
-			if self.chr:
-				if self.chr == 'X' or self.chr == 'x':
-					self.chr = '20'
-				self.chr = int(self.chr)
-		except:
-			pass
-		
-		self.readGeno()
-
-	def  readGeno(self):
-		try:
-			table = [['Chr'] + ['Locus'] + self.strainList]
-			if self.chr:
-				chr = self.dataset[self.chr-1]
-				for locus in chr:
-					items = string.split(string.join(locus.genotext, " "))
-					items = [chr.name] + [locus.name] + items
-					table += [items]
-			else:
-				for chr in self.dataset:
-					for locus in chr:
-						items = string.split(string.join(locus.genotext, " "))
-						items = [chr.name] + [locus.name] + items
-						table += [items]
-			if self.format == 'col':
-				table = [[r[col] for r in table] for col in range(1, len(table[0]))]
-				table[0][0] = 'Line'
-			lines = string.join(map(lambda x: string.join(x, '\t'), table), '\n')
-			self.contents.append(lines)
-		except:	
-			self.contents =['###Error: Read file error or name of chromosome is incorrect']
-			#traceback.print_exc()	
-			return
-
-		
-			
-- 
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