diff options
| -rw-r--r-- | wqflask/maintenance/dataset/probesets.py | 38 | ||||
| -rw-r--r-- | wqflask/maintenance/dataset/specials.py | 56 |
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") |