aboutsummaryrefslogtreecommitdiff
path: root/web/webqtl/textUI/cmdInterval.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/cmdInterval.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/webqtl/textUI/cmdInterval.py')
-rwxr-xr-xweb/webqtl/textUI/cmdInterval.py174
1 files changed, 174 insertions, 0 deletions
diff --git a/web/webqtl/textUI/cmdInterval.py b/web/webqtl/textUI/cmdInterval.py
new file mode 100755
index 00000000..0b97c7c3
--- /dev/null
+++ b/web/webqtl/textUI/cmdInterval.py
@@ -0,0 +1,174 @@
+# 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
+
+#########################################
+# Interval Mapping Class
+#########################################
+class cmdInterval(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
+
+
+ self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
+ if self.accessError:
+ return
+ self.sort = None
+ self.step = 0.01
+ self.peak = 1
+ self.chr = None
+ self.sort = None
+ self.returnnumber = 20
+ if self.error:
+ self.error = 1
+ self.contents.append(self.example)
+ return
+ else:
+ try:
+ self.sort = self.data.getvalue('sort')
+ if string.lower(self.sort) == 'pos':
+ self.sort = 'pos'
+ else:
+ self.sort = 'lrs'
+ except:
+ self.sort = None
+
+ try:
+ self.returnnumber = int(self.data.getvalue('return'))
+ except:
+ self.returnnumber = 20
+ try:
+ self.chr = self.data.getvalue('chr')
+ except:
+ self.chr = None
+
+ self.readDB()
+
+ def readDB(self):
+ prefix, dbId = self.getDBId(self.database)
+ if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
+ self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+ RISet = self.getRISet(prefix, dbId)
+ traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
+ if not traitdata:
+ self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
+ self.contents.append(self.example)
+ self.contents.append(self.accessCode)
+ return
+
+ dataset0 = reaper.Dataset()
+ dataset0.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
+ strainList = list(dataset0.prgy)
+ dataset = dataset0.addinterval()
+ if self.chr != None:
+ for _chr in dataset:
+ if string.lower(_chr.name) == string.lower(self.chr):
+ dataset.chromosome = [_chr]
+ break
+
+ strains = []
+ trait = []
+ _prgy = dataset.prgy
+ for item in traitdata:
+ if item[0] in _prgy:
+ strains.append(item[0])
+ trait.append(item[1])
+
+ qtlscan = dataset.regression(strains, trait)
+ LRS = dataset.permutation(strains, trait)
+ nperm = len(LRS)
+
+ #print inter1[0]
+ returnPeak = []
+ nqtl = len(qtlscan)
+ if self.peak:
+ for i in range(nqtl):
+ if i == 0 or qtlscan[i].locus.chr != qtlscan[i-1].locus.chr:
+ if qtlscan[i].lrs < qtlscan[i+1].lrs:
+ continue
+ elif i == nqtl-1 or qtlscan[i].locus.chr != qtlscan[i+1].locus.chr:
+ if qtlscan[i].lrs < qtlscan[i-1].lrs:
+ continue
+ else:
+ if qtlscan[i].lrs < qtlscan[i+1].lrs or qtlscan[i].lrs < qtlscan[i-1].lrs:
+ continue
+ returnPeak.append(qtlscan[i])
+ else:
+ returnPeak = qtlscan[:]
+
+ if returnPeak:
+ self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value\tcM")
+ qtlresult = []
+ for item in returnPeak:
+ p_value = reaper.pvalue(item.lrs,LRS)
+ qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value, item.locus.cM))
+ if self.sort == 'lrs':
+ qtlresult.sort(self.cmpLRS2)
+ for item in qtlresult:
+ self.contents.append("%s\t%2.4f\t%s\t%2.4f\t%1.4f\t%s" % item)
+ else:
+ self.contents.append("###Error: Error occurs while regression.")
+ return
+
+ def cmpPValue(self,A,B):
+ try:
+ if A[-1] > B[-1]:
+ return 1
+ elif A[-1] == B[-1]:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+ def cmpLRS2(self,A,B):
+ try:
+ if A[1] < B[1]:
+ return 1
+ elif A[1] == B[1]:
+ return 0
+ else:
+ return -1
+ except:
+ return 0
+
+