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-rw-r--r--issues/fetch_trait_data_using_genofiles.gmi42
1 files changed, 21 insertions, 21 deletions
diff --git a/issues/fetch_trait_data_using_genofiles.gmi b/issues/fetch_trait_data_using_genofiles.gmi
index 1108166..084513a 100644
--- a/issues/fetch_trait_data_using_genofiles.gmi
+++ b/issues/fetch_trait_data_using_genofiles.gmi
@@ -26,12 +26,12 @@ GROUP: BXD
### TODOS
-[x] indentify all required fields for this
-[x] code implementation
-[ ] handling null values
+* [x] indentify all required fields for this
+* [x] code implementation
+* [ ] handling null values
-Documented for Probeset,Genoset and PublishData
+## Documentation for Probeset,Genoset and Publish data types
### Publish Dataset
@@ -52,8 +52,9 @@ FROM CaseAttributeXRefNew cxref LEFT JOIN CaseAttribute ca
ON ca.Id = cxref.CaseAttributeId
GROUP BY InbredSetId, cxref.StrainId) B ON A.StrainId = B.StrainId
LIMIT 5;
-//results
+```
+```sql
+--------+-----------+------+-------+----------------------------------------------------------------+
| Sample | Value | SE | Count | CaseAttributes |
+--------+-----------+------+-------+----------------------------------------------------------------+
@@ -62,11 +63,11 @@ LIMIT 5;
| BXD12 | 16.000000 | 0.86 | x | Status=Live,Strain=BXD12,RRID=JAX:000045,Epoch=1,SeqCvge=43 |
+--------+-----------+------+-------+----------------------------------------------------------------+
+```
fetching specific trait sample data and case attributes for Publish using the parsed genofiles
-``` sql
-
+```sql
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
FROM
@@ -83,12 +84,13 @@ Order BY
Strain.Name
```
-### Probeset Dataset
-Dataset:Exon,
+### Probeset
+Example for
+Dataset_name:Exon,
Dataset_id:206
trait:4336695
-```sql
+```sql
SELECT Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2,B.CaseAttributes
FROM
(ProbeSetData, ProbeSetFreeze,
@@ -111,6 +113,9 @@ ProbeSetXRef.DataId = ProbeSetData.Id AND
ProbeSetData.StrainId = Strain.Id
Order BY
Strain.Name;
+```
+
+```sql
//results
+--------------+---------+----------+-------+--------------+-----------------------------------------------------------------+
@@ -121,9 +126,11 @@ Strain.Name;
| AKR/J | 6.2494 | 0.01774 | NULL | AKR/J | NULL |
| B6D2F1 | 6.50013 | 0.175722 | NULL | B6D2F1 | Status=Live,Strain=B6D2F1,RRID=JAX:100006,Epoch=0,SeqCvge= |
```
+
+
Fetch specific traits
-```sql
+```sql
SELECT
Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
FROM
@@ -138,20 +145,17 @@ ProbeSetXRef.DataId = ProbeSetData.Id AND
ProbeSetData.StrainId = Strain.Id
Order BY
Strain.Name
-
```
-```
for count
```sql
SELECT COUNT(*) QUERY_STATEMENT
```
-
### Genotype
-
to fetch trait and dataset samples + case attributes
-``` sql
+
+```sql
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
FROM (GenoData, GenoFreeze, Strain, GenoXRef)
@@ -170,7 +174,7 @@ LIMIT 5;
```
individual trait
-```
+```sql
SELECT
Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
@@ -186,7 +190,6 @@ individual trait
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
-
```
@@ -200,7 +203,6 @@ FROM CaseAttribute, CaseAttributeXRefNew
WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
AND CaseAttributeXRefNew.InbredSetId = %s
ORDER BY CaseAttribute.Id'''
-
%s -> requires id for the group for example BXD->1
```
@@ -215,9 +217,7 @@ AND CaseAttributeXRefNew.StrainId = Strain.Id
AND InbredSet.Id = CaseAttributeXRefNew.InbredSetId
AND CaseAttributeXRefNew.InbredSetId = 1
ORDER BY SampleName
-
fetch sample case attributes for bxd
-
```