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authorLei Yan2014-02-05 13:43:34 -0600
committerLei Yan2014-02-05 13:43:34 -0600
commit94b5018690f73cfad133d2d4c81ca0e8d4a7a7d4 (patch)
tree5b9e07d648e891486f065140f9d9f58bba143054 /wqflask/maintenance
parentc30c4ed7afaf6e312476506a63db74541d019260 (diff)
downloadgenenetwork2-94b5018690f73cfad133d2d4c81ca0e8d4a7a7d4.tar.gz
On branch master
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/dataset/probesets.py38
-rw-r--r--wqflask/maintenance/dataset/specials.py56
2 files changed, 50 insertions, 44 deletions
diff --git a/wqflask/maintenance/dataset/probesets.py b/wqflask/maintenance/dataset/probesets.py
index d87240a2..97bb5bdf 100644
--- a/wqflask/maintenance/dataset/probesets.py
+++ b/wqflask/maintenance/dataset/probesets.py
@@ -1,5 +1,3 @@
-import sys
-
import utilities
import datastructure
import genotypes
@@ -90,39 +88,3 @@ def get_normalized_probeset(locus, inbredsetid):
#
normalized_probesets.append(normalized_probeset)
return normalized_probesets
-
-locus="rs3663871"
-inbredsetid=1
-
-results = get_normalized_probeset(locus=locus, inbredsetid=inbredsetid)
-file = open('probesets_%s.txt' % (locus), 'w+')
-file.write("GN Dataset ID\t")
-file.write("Dataset Full Name\t")
-file.write("ProbeSet Name\t")
-file.write("Symbol\t")
-file.write("ProbeSet Description\t")
-file.write("Probe Target Description\t")
-file.write("ProbeSet Chr\t")
-file.write("ProbeSet Mb\t")
-file.write("Mean\t")
-file.write("LRS\t")
-file.write("Geno Chr\t")
-file.write("Geno Mb\t")
-file.write("\n")
-file.flush()
-for row in results:
- file.write("%s\t" % (row[0]))
- file.write("%s\t" % (utilities.clearspaces(row[2], default='')))
- file.write("%s\t" % (utilities.clearspaces(row[3], default='')))
- file.write("%s\t" % (utilities.clearspaces(row[4], default='')))
- file.write("%s\t" % (utilities.clearspaces(row[5], default='')))
- file.write("%s\t" % (utilities.clearspaces(row[6], default='')))
- file.write("%s\t" % (utilities.clearspaces(row[7], default='')))
- file.write("%s\t" % (row[8]))
- file.write("%s\t" % (row[9]))
- file.write("%s\t" % (row[10]))
- file.write("%s\t" % (utilities.clearspaces(row[11], default='')))
- file.write("%s\t" % (row[12]))
- file.write('\n')
- file.flush()
-file.close()
diff --git a/wqflask/maintenance/dataset/specials.py b/wqflask/maintenance/dataset/specials.py
index 52a2389f..90ab1c5f 100644
--- a/wqflask/maintenance/dataset/specials.py
+++ b/wqflask/maintenance/dataset/specials.py
@@ -3,6 +3,52 @@ import genotypes
import probesets
"""
+For: Rob, GeneNetwork
+Date: 2014-02-04
+Function:
+ For BXD group, fetch probesets with given locus.
+
+locus="rs3663871"
+"""
+def bxd_probesets_locus(locus):
+ #
+ inbredsetid=1
+ #
+ file = open('probesets_%s.txt' % (locus), 'w+')
+ file.write("GN Dataset ID\t")
+ file.write("Dataset Full Name\t")
+ file.write("ProbeSet Name\t")
+ file.write("Symbol\t")
+ file.write("ProbeSet Description\t")
+ file.write("Probe Target Description\t")
+ file.write("ProbeSet Chr\t")
+ file.write("ProbeSet Mb\t")
+ file.write("Mean\t")
+ file.write("LRS\t")
+ file.write("Geno Chr\t")
+ file.write("Geno Mb\t")
+ file.write("\n")
+ file.flush()
+ #
+ results = get_normalized_probeset(locus=locus, inbredsetid=inbredsetid)
+ for row in results:
+ file.write("%s\t" % (row[0]))
+ file.write("%s\t" % (utilities.clearspaces(row[2], default='')))
+ file.write("%s\t" % (utilities.clearspaces(row[3], default='')))
+ file.write("%s\t" % (utilities.clearspaces(row[4], default='')))
+ file.write("%s\t" % (utilities.clearspaces(row[5], default='')))
+ file.write("%s\t" % (utilities.clearspaces(row[6], default='')))
+ file.write("%s\t" % (utilities.clearspaces(row[7], default='')))
+ file.write("%s\t" % (row[8]))
+ file.write("%s\t" % (row[9]))
+ file.write("%s\t" % (row[10]))
+ file.write("%s\t" % (utilities.clearspaces(row[11], default='')))
+ file.write("%s\t" % (row[12]))
+ file.write('\n')
+ file.flush()
+ file.close()
+
+"""
For: Ash
Date: 2014-02-05
Function:
@@ -50,16 +96,14 @@ def bxd_correlations():
probesetid = probesetxref[0]
probesetdataid = probesetxref[1]
probeset = probesets.get_probeset(probesetid)
- ProbeSetId = probeset[0]
- ProbeSetName = probeset[1]
- # Geno Name Overlap Number Pearson r Pearson p Spearman r Spearman p
+ probesetname = probeset[1]
probesetdata = probesets.get_probesetdata(probesetdataid)
#
for geno in genos:
genoname = geno['locus']
- outputfile.write("%s\t" % probeSetid)
- outputfile.write("%s\t" % ProbeSetName)
- outputfile.write("%s\t" % GenoName)
+ outputfile.write("%s\t" % probesetid)
+ outputfile.write("%s\t" % probesetname)
+ outputfile.write("%s\t" % genoname)
outputfile.write("%s\t" % "Overlap Number")
outputfile.write("%s\t" % "Pearson r")
outputfile.write("%s\t" % "Pearson p")