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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
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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