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authorLei Yan2014-02-10 14:59:27 -0600
committerLei Yan2014-02-10 14:59:27 -0600
commita260db93da548ce7511521c5f63c03c3d279bcb1 (patch)
tree50965c7995bdadc6b104fa05f074d7494e1d872e /wqflask/maintenance
parent4093f244cad0bd5ba21412acd9dfd1589db2d761 (diff)
downloadgenenetwork2-a260db93da548ce7511521c5f63c03c3d279bcb1.tar.gz
On branch master
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/dataset/specials.py129
-rw-r--r--wqflask/maintenance/dataset/specials1.py53
-rw-r--r--wqflask/maintenance/dataset/specials2.py109
3 files changed, 162 insertions, 129 deletions
diff --git a/wqflask/maintenance/dataset/specials.py b/wqflask/maintenance/dataset/specials.py
deleted file mode 100644
index 4ff85333..00000000
--- a/wqflask/maintenance/dataset/specials.py
+++ /dev/null
@@ -1,129 +0,0 @@
-import utilities
-import datastructure
-import genotypes
-import probesets
-import calculate
-
-"""
-For: Rob, GeneNetwork
-Date: 2014-02-04
-Function:
- For BXD group, fetch probesets with given locus (mapping info).
-
-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 "From geno file, get %d strains" % (len(genostrains))
- print "From geno file, get %d genos" % (len(genos))
- #
- probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
- print "From DB, 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)
- probesetdata = zip(*probesetdata)
- probesetdata = utilities.to_dic([strain.lower() for strain in probesetdata[1]], probesetdata[2])
- #
- for geno in genos:
- genoname = geno['locus']
- outputfile.write("%s\t" % probesetid)
- outputfile.write("%s\t" % probesetname)
- outputfile.write("%s\t" % genoname)
- #
- dic1 = geno['dicvalues']
- dic2 = probesetdata
- keys, values1, values2 = utilities.overlap(dic1, dic2)
- rs = calculate.correlation(values1, values2)
- #
- outputfile.write("%s\t" % len(keys))
- outputfile.write("%s\t" % rs[0][0])
- outputfile.write("%s\t" % rs[0][1])
- outputfile.write("%s\t" % rs[1][0])
- outputfile.write("%s\t" % rs[1][1])
- outputfile.write("\n")
- outputfile.flush()
- #
- outputfile.close()
-
-bxd_correlations()
diff --git a/wqflask/maintenance/dataset/specials1.py b/wqflask/maintenance/dataset/specials1.py
new file mode 100644
index 00000000..9159fd7f
--- /dev/null
+++ b/wqflask/maintenance/dataset/specials1.py
@@ -0,0 +1,53 @@
+import utilities
+import datastructure
+import genotypes
+import probesets
+import calculate
+
+"""
+For: Rob, GeneNetwork
+Date: 2014-02-04
+Function:
+ For BXD group, fetch probesets with given locus (mapping info).
+
+locus="rs3663871"
+"""
+def bxd_probesets_locus(locus, 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()
+ #
+ results = probesets.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()
+
+locus='rs3663871'
+inbredsetid=1
+bxd_probesets_locus(locus=locus, inbredsetid=inbredsetid)
diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py
new file mode 100644
index 00000000..2acfd2ef
--- /dev/null
+++ b/wqflask/maintenance/dataset/specials2.py
@@ -0,0 +1,109 @@
+import utilities
+import datastructure
+import genotypes
+import probesets
+import calculate
+
+"""
+For: Ash
+Date: 2014-02-07
+Function:
+ For BXD group, get a probesetfreeze name list.
+"""
+def probesetfreeze_list():
+ #
+ inbredsetid = 1
+ outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output"
+ #
+ probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
+ print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
+ file = open(outputdir + '/' + 'probesetfreezes.txt', 'w+')
+ #
+ for probesetfreeze in probesetfreezes:
+ #
+ print probesetfreeze
+ probesetfreezeid = probesetfreeze[0]
+ probesetfreezename = probesetfreeze[1]
+ probesetfreezefullname = probesetfreeze[2]
+ #
+ file.write("%s\t" % probesetfreezeid)
+ file.write("%s" % probesetfreezefullname)
+ file.write("\n")
+ file.flush()
+ #
+ file.close()
+
+"""
+For: Ash
+Date: 2014-02-05
+Function:
+ For BXD group, calculate correlations with genotypes and probesets.
+"""
+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 "From geno file, get %d strains" % (len(genostrains))
+ print "From geno file, get %d genos" % (len(genos))
+ #
+ probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
+ print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
+ for probesetfreeze in probesetfreezes:
+ correlations(genos, probesetfreeze)
+
+def correlations(genos, probesetfreeze):
+ 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)
+ probesetdata = zip(*probesetdata)
+ probesetdata = utilities.to_dic([strain.lower() for strain in probesetdata[1]], probesetdata[2])
+ #
+ for geno in genos:
+ genoname = geno['locus']
+ outputfile.write("%s\t" % probesetid)
+ outputfile.write("%s\t" % probesetname)
+ outputfile.write("%s\t" % genoname)
+ #
+ dic1 = geno['dicvalues']
+ dic2 = probesetdata
+ keys, values1, values2 = utilities.overlap(dic1, dic2)
+ rs = calculate.correlation(values1, values2)
+ #
+ outputfile.write("%s\t" % len(keys))
+ outputfile.write("%s\t" % rs[0][0])
+ outputfile.write("%s\t" % rs[0][1])
+ outputfile.write("%s\t" % rs[1][0])
+ outputfile.write("%s\t" % rs[1][1])
+ outputfile.write("\n")
+ outputfile.flush()
+ #
+ outputfile.close() \ No newline at end of file