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| author | Lei Yan | 2014-02-04 11:35:41 -0600 |
|---|---|---|
| committer | Lei Yan | 2014-02-04 11:35:41 -0600 |
| commit | ad07fc167c4f35490fd59e687aac1f4291defcc2 (patch) | |
| tree | 725b7a446036269d895c6ff34c14c45218e9c55d /wqflask/maintenance/dataset | |
| parent | 2c6abd47b78bea42423aa45f417897525f63f8a2 (diff) | |
| download | genenetwork2-ad07fc167c4f35490fd59e687aac1f4291defcc2.tar.gz | |
On branch master
Diffstat (limited to 'wqflask/maintenance/dataset')
| -rw-r--r-- | wqflask/maintenance/dataset/genotypes.py | 13 | ||||
| -rw-r--r-- | wqflask/maintenance/dataset/probesets.py | 18 |
2 files changed, 28 insertions, 3 deletions
diff --git a/wqflask/maintenance/dataset/genotypes.py b/wqflask/maintenance/dataset/genotypes.py new file mode 100644 index 00000000..c83fb8b7 --- /dev/null +++ b/wqflask/maintenance/dataset/genotypes.py @@ -0,0 +1,13 @@ +import utilities + +def get_geno(inbredsetid, name): + cursor = utilities.get_cursor() + sql = """ + SELECT Geno.`Id`, Geno.`Name`, Geno.`Chr`, Geno.`Mb` + FROM (Geno, InbredSet) + WHERE Geno.`SpeciesId`=InbredSet.`SpeciesId` + AND InbredSet.`Id`=%s + AND Geno.`Name` LIKE %s + """ + cursor.execute(sql, (inbredsetid, name)) + return cursor.fetchone() diff --git a/wqflask/maintenance/dataset/probesets.py b/wqflask/maintenance/dataset/probesets.py index 2c755203..06b9a394 100644 --- a/wqflask/maintenance/dataset/probesets.py +++ b/wqflask/maintenance/dataset/probesets.py @@ -1,6 +1,7 @@ import sys import utilities +import genotypes def get_probesetxref(probesetfreezeid): cursor = utilities.get_cursor() @@ -47,7 +48,7 @@ def get_probesetxref_probesetfreezeid(locus, probesetfreezeid): def get_probesetxref_inbredsetid(locus, inbredsetid): cursor = utilities.get_cursor() sql = """ - SELECT ProbeSetXRef.`ProbeSetId` + SELECT ProbeSetXRef.`ProbeSetId`, ProbeSetXRef.`mean`, ProbeSetXRef.`LRS`, ProbeSetXRef.`Locus` FROM (ProbeSetXRef, ProbeSetFreeze, ProbeFreeze) WHERE ProbeSetXRef.`ProbeSetFreezeId`=ProbeSetFreeze.`Id` AND ProbeSetFreeze.`ProbeFreezeId`=ProbeFreeze.`Id` @@ -64,8 +65,19 @@ def get_normalized_probeset(locus, inbredsetid): normalized_probeset = [] probesetid = probesetxref[0] probeset = get_probeset(probesetid) - normalized_probeset.append(probeset) + normalized_probeset.append(probeset[1]) + normalized_probeset.append(probeset[2]) + normalized_probeset.append(probeset[3]) + 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 + print normalized_probesets[:2] get_normalized_probeset(locus="rs3663871", inbredsetid=1) |