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Diffstat (limited to 'wqflask/maintenance/dataset/specials1.py')
| -rw-r--r-- | wqflask/maintenance/dataset/specials1.py | 53 |
1 files changed, 53 insertions, 0 deletions
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) |