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diff --git a/scripts/maintenance/README.txt b/scripts/maintenance/README.txt new file mode 100644 index 00000000..8604a5c9 --- /dev/null +++ b/scripts/maintenance/README.txt @@ -0,0 +1,66 @@ +Theses are Python2 scripts used for uploading data into the MySQL +database (current as per April 2018) + + +Last updated by A.Centeno 4-2-18 +========================== +load_genotypes.py +========================== +Mainly used to enter genotype batch records +Run load_genotypes.py as: +python delete_genotypes.py /home/acenteno/copyfrom_spring211/Maintenance/dataset/Arthur-Geno-Pheno-Data/Load_Genotypes/config.ini + +========================== +delete_genotypes.py +========================== +Mainly used to delete genotype batch records +Run delete_genotypes.py as: +python delete_genotypes.py /home/acenteno/copyfrom_spring211/Maintenance/dataset/Arthur-Geno-Pheno-Data/Delete_Genotypes/config.ini + +========================== +load_phenotypes.py +========================== +Mainly used to enter phenotype trait batch records +Run load_phenotypes.py as: +python load_phenotypes.py /home/acenteno/copyfrom_spring211/Maintenance/dataset/Arthur-Geno-Pheno-Data/Load_Phenotypes/config.ini + +========================== +delete_phenotypes.py +========================== +Mainly used to delete phenotype trait full records +Run delete_phenotypes.py as: +python delete_phenotypes.py /home/acenteno/copyfrom_spring211/Maintenance/dataset/Arthur-Geno-Pheno-Data/Delete_Phenotypes/config.ini + +========================== +QTL_Reaper_v6.py +========================== +Mainly used to perform QTL reaper and obtain Max LRS values. +Run QTL_Reaper_v6.py as: +python QTL_Reaper_v6.py (and GN accession number here) + +========================== +Update_Case_Attributes_MySQL_tab.py +========================== +Mainly used to enter Case attributes. +Run Update_Case_Attributes_MySQL_tab.py as: +python Update_Case_Attributes_MySQL_tab.py + +========================== +readProbeSetMean_v7.py +========================== +Mainly used to enter mean expression data. +Run readProbeSetMean_v7.py as: +python readProbeSetMean_v7.py + +========================== +readProbeSetSE_v7.py +========================== +Mainly used to enter Standard Error values from expression data. +Run readProbeSetSE_v7.py as: +python readProbeSetSE_v7.py + +========================== +MYSQL command CALCULATE MEANS NEW Structure: +========================== +Mainly used to calculate mean from expression data values. +update ProbeSetXRef set mean = (select AVG(value) from ProbeSetData where ProbeSetData.Id = ProbeSetXRef.DataId) where ProbeSetXRef.ProbeSetFreezeId = 811; |