aboutsummaryrefslogtreecommitdiff
path: root/web/webqtl/textUI/cmdGeno.py
diff options
context:
space:
mode:
authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/textUI/cmdGeno.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/textUI/cmdGeno.py')
-rwxr-xr-xweb/webqtl/textUI/cmdGeno.py118
1 files changed, 118 insertions, 0 deletions
diff --git a/web/webqtl/textUI/cmdGeno.py b/web/webqtl/textUI/cmdGeno.py
new file mode 100755
index 00000000..8dd0f924
--- /dev/null
+++ b/web/webqtl/textUI/cmdGeno.py
@@ -0,0 +1,118 @@
+# 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
+
+
+