1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
import datastructure
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:
For BXD group, calculate correlations with genotypes and probesets.
Running History:
2014-02-05 /home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output
"""
def bxd_correlations():
#
inbredsetid = 1
genofile = "/home/leiyan/gn/web/genotypes/BXD.geno"
outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output"
#
t = genotypes.load_genos(genofile)
genostrains = t[0]
genos = t[1]
print "Get %d genos" % (len(genos))
#
probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
print "Get %d probesetfreezes" % (len(probesetfreezes))
#
for probesetfreeze in probesetfreezes:
#
print probesetfreeze
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
probesetfreezefullname = probesetfreeze[2]
#
outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+")
outputfile.write("%s\t" % "ProbeSet Id")
outputfile.write("%s\t" % "ProbeSet Name")
outputfile.write("%s\t" % "Geno Name")
outputfile.write("%s\t" % "Overlap Number")
outputfile.write("%s\t" % "Pearson r")
outputfile.write("%s\t" % "Pearson p")
outputfile.write("%s\t" % "Spearman r")
outputfile.write("%s\t" % "Spearman p")
outputfile.write("\n")
outputfile.flush()
#
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
print "Get %d probesetxrefs" % (len(probesetxrefs))
#
for probesetxref in probesetxrefs:
#
probesetid = probesetxref[0]
probesetdataid = probesetxref[1]
probeset = probesets.get_probeset(probesetid)
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" % "Overlap Number")
outputfile.write("%s\t" % "Pearson r")
outputfile.write("%s\t" % "Pearson p")
outputfile.write("%s\t" % "Spearman r")
outputfile.write("%s\t" % "Spearman p")
outputfile.write("\n")
outputfile.flush()
#
outputfile.close()
bxd_correlations()
|
