MAGENTApy

Experimental port of MAGENTA software to Python. https://www.broadinstitute.org/mpg/magenta/

Not fully tested yet!

Note: For maintainability, this script is intentionally un-pythonic, following the original code structure of MAGENTA written in MATLAB.

Usage

git clone https://github.com/mkanai/MAGENTApy.git
cd MAGENTApy
python Run_MAGENTA.py

Edit config.yml, or specify your own configuration by --config myconfig.yml. All parameters are compatible with the original MAGENTA.

MAGENTA is copyright by Ayellet Segre, Mark Daly, and David Altshuler of The Broad Institute.

Name		Name	Last commit message	Last commit date
Latest commit History 16 Commits
MAGENTA		MAGENTA
.gitignore		.gitignore
AllHumanGeneChrPosStrand_RefSeq_hg19_072111		AllHumanGeneChrPosStrand_RefSeq_hg19_072111
AllHumanGeneNames_RefSeq_hg19_07-GO_terms_BioProc_MolFunc_db_immune.txt		AllHumanGeneNames_RefSeq_hg19_07-GO_terms_BioProc_MolFunc_db_immune.txt
AllHumanGeneNames_RefSeq_hg19_072111		AllHumanGeneNames_RefSeq_hg19_072111
CEU_HapMap_pruned_SNPs_ChrNumPos_hg19_072111		CEU_HapMap_pruned_SNPs_ChrNumPos_hg19_072111
DB-RA-DrugGene		DB-RA-DrugGene
GO_PANTHER_INGENUITY_KEGG_REACTOME_BIOCARTA		GO_PANTHER_INGENUITY_KEGG_REACTOME_BIOCARTA
GO_terms_BioProc_MolFunc_db		GO_terms_BioProc_MolFunc_db
GO_terms_BioProc_MolFunc_db_immune.txt		GO_terms_BioProc_MolFunc_db_immune.txt
GWAS_SNP_ChrNumPosZscoresPval_Example		GWAS_SNP_ChrNumPosZscoresPval_Example
GWAS_SNP_ChrNumPosZscoresPval_Example_SNPOR		GWAS_SNP_ChrNumPosZscoresPval_Example_SNPOR
GWAS_SNP_ChrNumPosZscoresPval_Example_SNPrs		GWAS_SNP_ChrNumPosZscoresPval_Example_SNPrs
INGENUITY_BIOCARTA		INGENUITY_BIOCARTA
PANTHER_INGENUITY_KEGG_REACTOME_BIOCARTA		PANTHER_INGENUITY_KEGG_REACTOME_BIOCARTA
README		README
README.md		README.md
RefFlatGeneSymbolGeneID_18434Genes_11-tmp.txt		RefFlatGeneSymbolGeneID_18434Genes_11-tmp.txt
RefFlatGeneSymbolGeneID_18434Genes_111909		RefFlatGeneSymbolGeneID_18434Genes_111909
Run_MAGENTA.py		Run_MAGENTA.py
config.yml		config.yml
hotspot_boundaries_b37_hg19_072111		hotspot_boundaries_b37_hg19_072111