diff options
Diffstat (limited to 'wqflask/maintenance/dataset/probesets.py')
| -rw-r--r-- | wqflask/maintenance/dataset/probesets.py | 18 |
1 files changed, 15 insertions, 3 deletions
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) |