diff options
| -rw-r--r-- | issues/fetch_trait_data_using_genofiles.gmi | 42 |
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 - ``` |