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author | Lei Yan | 2014-02-04 12:14:14 -0600 |
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committer | Lei Yan | 2014-02-04 12:14:14 -0600 |
commit | 839115abbdf1b7e90da1d4db7758a2f7f8f83037 (patch) | |
tree | 345cf6dc1f1e6545421e9111305826b3c5925a15 /wqflask/maintenance/dataset/probesets.py | |
parent | ad07fc167c4f35490fd59e687aac1f4291defcc2 (diff) | |
download | genenetwork2-839115abbdf1b7e90da1d4db7758a2f7f8f83037.tar.gz |
On branch master
Diffstat (limited to 'wqflask/maintenance/dataset/probesets.py')
-rw-r--r-- | wqflask/maintenance/dataset/probesets.py | 26 |
1 files changed, 23 insertions, 3 deletions
diff --git a/wqflask/maintenance/dataset/probesets.py b/wqflask/maintenance/dataset/probesets.py index 06b9a394..26d794a8 100644 --- a/wqflask/maintenance/dataset/probesets.py +++ b/wqflask/maintenance/dataset/probesets.py @@ -1,6 +1,7 @@ import sys import utilities +import datastructure import genotypes def get_probesetxref(probesetfreezeid): @@ -48,7 +49,7 @@ def get_probesetxref_probesetfreezeid(locus, probesetfreezeid): def get_probesetxref_inbredsetid(locus, inbredsetid): cursor = utilities.get_cursor() sql = """ - SELECT ProbeSetXRef.`ProbeSetId`, ProbeSetXRef.`mean`, ProbeSetXRef.`LRS`, ProbeSetXRef.`Locus` + SELECT ProbeSetXRef.`ProbeSetId`, ProbeSetXRef.`mean`, ProbeSetXRef.`LRS`, ProbeSetXRef.`Locus`, ProbeSetXRef.`ProbeSetFreezeId` FROM (ProbeSetXRef, ProbeSetFreeze, ProbeFreeze) WHERE ProbeSetXRef.`ProbeSetFreezeId`=ProbeSetFreeze.`Id` AND ProbeSetFreeze.`ProbeFreezeId`=ProbeFreeze.`Id` @@ -63,6 +64,13 @@ def get_normalized_probeset(locus, inbredsetid): probesetxrefs = get_probesetxref_inbredsetid(locus, inbredsetid) for probesetxref in probesetxrefs: normalized_probeset = [] + # + probesetfreezeid = probesetxref[4] + probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid) + normalized_probeset.append(probesetfreeze[0]) + normalized_probeset.append(probesetfreeze[1]) + normalized_probeset.append(probesetfreeze[2]) + # probesetid = probesetxref[0] probeset = get_probeset(probesetid) normalized_probeset.append(probeset[1]) @@ -71,13 +79,25 @@ def get_normalized_probeset(locus, inbredsetid): normalized_probeset.append(probeset[4]) normalized_probeset.append(probeset[5]) normalized_probeset.append(probeset[6]) + # normalized_probeset.append(probesetxref[1]) normalized_probeset.append(probesetxref[2]) + # locus = probesetxref[3] geno = genotypes.get_geno(inbredsetid=inbredsetid, name=locus) normalized_probeset.append(geno[2]) normalized_probeset.append(geno[3]) + # normalized_probesets.append(normalized_probeset) - print normalized_probesets[:2] -get_normalized_probeset(locus="rs3663871", inbredsetid=1) +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\n") +file.flush() +for row in results: + file.write(row[0]) + file.flush() +file.close() |