Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into testing

1 files changed, 66 insertions, 0 deletions

diff --git a/scripts/maintenance/README.txt b/scripts/maintenance/README.txt
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+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;