From ed4fec69cbf0aa3339a81d5964122fa3a9b196b5 Mon Sep 17 00:00:00 2001
From: Atemia <j.atemia@fz-juelich.de>
Date: Wed, 4 Dec 2024 15:57:31 +0100
Subject: [PATCH] chore: restructure directories and relocate final cleaned
 GWAS data

---
 .../gwas_data_3455_accessions/genotype/README.md               | 3 ---
 .../genotype/all_taxa_3455_accessions.hapmap.txt               | 3 ---
 .../genotype/diplo_per_geno_3455_accessions.hapmap.txt         | 3 ---
 .../diplo_plus_perennis_geno_3455_accessions.hapmap.txt        | 3 ---
 .../genotype/hue_geno_3455_accessions.hapmap.txt               | 3 ---
 .../genotype/lux_geno_3455_accessions.hapmap.txt               | 3 ---
 .../genotype/lux_plus_nica_geno_3455_accessions.hapmap.txt     | 3 ---
 .../genotype/mex_chalco_geno_3455_accessions.hapmap.txt        | 3 ---
 .../genotype/mex_durango_geno_3455_accessions.hapmap.txt       | 3 ---
 .../genotype/mex_geno_3455_accessions.hapmap.txt               | 3 ---
 .../gwas_data_3455_accessions/genotype/mex_hapmap_101.txt      | 0
 .../genotype/mex_mesa_central_geno_3455_accessions.hapmap.txt  | 3 ---
 .../genotype/mex_nobogame_geno_3455_accessions.hapmap.txt      | 3 ---
 .../genotype/nica_geno_3455_accessions.hapmap.txt              | 3 ---
 .../genotype/parv_geno_3455_accessions.hapmap.txt              | 3 ---
 .../genotype/parv_plus_hue_geno_3455_accessions.hapmap.txt     | 3 ---
 .../genotype/per_geno_3455_accessions.hapmap.txt               | 3 ---
 .../genotype_h5/.ipynb_checkpoints/Untitled-checkpoint.ipynb   | 3 ---
 .../gwas_data_3455_accessions/genotype_h5/README.md            | 3 ---
 .../gwas_data_3455_accessions/genotype_h5/Untitled.ipynb       | 3 ---
 .../genotype_h5/all_taxa_3455_accessions.hapmap                | 3 ---
 .../genotype_h5/diplo_per_geno_3455_accessions.hapmap          | 3 ---
 .../gwas_data_3455_accessions/genotype_h5/example.h5           | 3 ---
 .../genotype_h5/hue_geno_3455_accessions.hapmap                | 3 ---
 .../genotype_h5/lux_geno_3455_accessions.hapmap                | 3 ---
 .../genotype_h5/mex_chalco_geno_3455_accessions.hapmap         | 3 ---
 .../genotype_h5/mex_durango_geno_3455_accessions.hapmap        | 3 ---
 .../genotype_h5/mex_geno_3455_accessions.hapmap                | 3 ---
 .../genotype_h5/mex_mesa_central_geno_3455_accessions.hapmap   | 3 ---
 .../genotype_h5/mex_nobogame_geno_3455_accessions.hapmap       | 3 ---
 .../genotype_h5/nica_geno_3455_accessions.hapmap               | 3 ---
 .../genotype_h5/parv_geno_3455_accessions.hapmap.h5            | 3 ---
 .../genotype_h5/per_geno_3455_accessions.hapmap                | 3 ---
 .../genotype_imputed/HDF5/all_imputed_missing_hetero.HDF5      | 3 ---
 .../HDF5/diplo_per_imputed_missing_hetero.HDF5                 | 3 ---
 .../HDF5/diplo_plus_perennis_imputed_missing_hetero.HDF5       | 3 ---
 .../genotype_imputed/HDF5/hue_imputed_missing_hetero.HDF5      | 3 ---
 .../HDF5/mex_chalco_imputed_missing_hetero.HDF5                | 3 ---
 .../HDF5/mex_durango_imputed_missing_hetero.HDF5               | 3 ---
 .../genotype_imputed/HDF5/mex_imputed_missing_hetero.HDF5      | 3 ---
 .../genotype_imputed/HDF5/mex_mesa_imputed_missing_hetero.h5   | 3 ---
 .../HDF5/mex_nobogame_imputed_missing_hetero.HDF5              | 3 ---
 .../genotype_imputed/HDF5/nica_imputed_missing_hetero.HDF5     | 3 ---
 .../genotype_imputed/HDF5/parv_imputed_missing_hetero.HDF5     | 3 ---
 .../HDF5/parv_plus_hue_imputed_missing_hetero.HDF5             | 3 ---
 .../genotype_imputed/HDF5/per_imputed_missing_hetero.HDF5      | 3 ---
 .../hapmap/all_imputed_missing_hetero.hapmap.txt               | 3 ---
 .../hapmap/diplo_per_imputed_missing_hetero.hapmap.txt         | 3 ---
 .../diplo_plus_perennis_imputed_missing_hetero.hapmap.txt      | 3 ---
 .../hapmap/hue_imputed_missing_hetero.hapmap.txt               | 3 ---
 .../hapmap/mex_chalco_imputed_missing_hetero.hapmap.txt        | 3 ---
 .../hapmap/mex_durango_imputed_missing_hetero.hapmap.txt       | 3 ---
 .../hapmap/mex_imputed_missing_hetero.hapmap.txt               | 3 ---
 .../hapmap/mex_mesa_imputed_missing_hetero.hapmap.txt          | 3 ---
 .../hapmap/mex_nobogame_imputed_missing_hetero.hapmap.txt      | 3 ---
 .../hapmap/nica_imputed_missing_hetero.hapmap.txt              | 3 ---
 .../hapmap/parv_imputed_missing_hetero.hapmap.txt              | 3 ---
 .../hapmap/parv_plus_hue_imputed_missing_hetero.hapmap.txt     | 3 ---
 .../hapmap/per_imputed_missing_hetero.hapmap.txt               | 3 ---
 .../plink/all_imputed_missing_hetero.plink.plk.map             | 3 ---
 .../plink/all_imputed_missing_hetero.plink.plk.ped             | 3 ---
 .../plink/diplo_per_imputed_missing_hetero.plink.plk.map       | 3 ---
 .../plink/diplo_per_imputed_missing_hetero.plink.plk.ped       | 3 ---
 .../diplo_plus_perennis_imputed_missing_hetero.plink.plk.map   | 3 ---
 .../diplo_plus_perennis_imputed_missing_hetero.plink.plk.ped   | 3 ---
 .../plink/hue_imputed_missing_hetero.plink.plk.map             | 3 ---
 .../plink/hue_imputed_missing_hetero.plink.plk.ped             | 3 ---
 .../plink/mex_chalco_imputed_missing_hetero.plink.plk.map      | 3 ---
 .../plink/mex_chalco_imputed_missing_hetero.plink.plk.ped      | 3 ---
 .../plink/mex_durango_imputed_missing_hetero.plink.plk.map     | 3 ---
 .../plink/mex_durango_imputed_missing_hetero.plink.plk.ped     | 3 ---
 .../plink/mex_imputed_missing_hetero.plink.plk.map             | 3 ---
 .../plink/mex_imputed_missing_hetero.plink.plk.ped             | 3 ---
 .../plink/mex_mesa_imputed_missing_hetero.plink.plk.map        | 3 ---
 .../plink/mex_mesa_imputed_missing_hetero.plink.plk.ped        | 3 ---
 .../plink/mex_nobogame_imputed_missing_hetero.plink.plk.map    | 3 ---
 .../plink/mex_nobogame_imputed_missing_hetero.plink.plk.ped    | 3 ---
 .../plink/nica_imputed_missing_hetero.plink.plk.map            | 3 ---
 .../plink/nica_imputed_missing_hetero.plink.plk.ped            | 3 ---
 .../plink/parv_imputed_missing_hetero.plink.plk.map            | 3 ---
 .../plink/parv_imputed_missing_hetero.plink.plk.ped            | 3 ---
 .../plink/parv_plus_hue_imputed_missing_hetero.plink.plk.map   | 3 ---
 .../plink/parv_plus_hue_imputed_missing_hetero.plink.plk.ped   | 3 ---
 .../plink/per_imputed_missing_hetero.plink.plk.map             | 3 ---
 .../plink/per_imputed_missing_hetero.plink.plk.ped             | 3 ---
 .../genotype_numeric/all_numeric.hapmap.txt                    | 3 ---
 .../genotype_numeric/diplo_per_numeric.hapmap.txt              | 3 ---
 .../genotype_numeric/diplo_plus_perennis_numeric.hapmap.txt    | 3 ---
 .../genotype_numeric/hue_numeric.hapmap.txt                    | 3 ---
 .../genotype_numeric/mex_chalco_numeric.hapmap.txt             | 3 ---
 .../genotype_numeric/mex_durango_numeric.hapmap.txt            | 3 ---
 .../genotype_numeric/mex_mesa_numeric.hapmap.txt               | 3 ---
 .../genotype_numeric/mex_nobogame_numeric.hapmap.txt           | 3 ---
 .../genotype_numeric/mex_numeric.hapmap.txt                    | 3 ---
 .../genotype_numeric/nica_numeric.hapmap.txt                   | 3 ---
 .../genotype_numeric/parv_numeric.hapmap.txt                   | 3 ---
 .../genotype_numeric/parv_plus_hue_numeric.hapmap.txt          | 3 ---
 .../genotype_numeric/per_numeric.hapmap.txt                    | 3 ---
 .../genotype_plink/.fuse_hidden0003c72500000002                | 3 ---
 .../genotype_plink/.fuse_hidden0003c72700000001                | 3 ---
 .../genotype_plink/all_taxa_3455_accessions.hapmap.plk.bed     | 3 ---
 .../genotype_plink/all_taxa_3455_accessions.hapmap.plk.bim     | 3 ---
 .../genotype_plink/all_taxa_3455_accessions.hapmap.plk.fam     | 3 ---
 .../genotype_plink/all_taxa_3455_accessions.hapmap.plk.log     | 3 ---
 .../genotype_plink/all_taxa_3455_accessions.hapmap.plk.map     | 3 ---
 .../genotype_plink/all_taxa_3455_accessions.hapmap.plk.nosex   | 3 ---
 .../genotype_plink/all_taxa_3455_accessions.hapmap.plk.ped     | 3 ---
 .../diplo_per_geno_3455_accessions.hapmap.plk.bed              | 3 ---
 .../diplo_per_geno_3455_accessions.hapmap.plk.bim              | 3 ---
 .../diplo_per_geno_3455_accessions.hapmap.plk.fam              | 3 ---
 .../diplo_per_geno_3455_accessions.hapmap.plk.log              | 3 ---
 .../diplo_per_geno_3455_accessions.hapmap.plk.map              | 3 ---
 .../diplo_per_geno_3455_accessions.hapmap.plk.nosex            | 3 ---
 .../diplo_per_geno_3455_accessions.hapmap.plk.ped              | 3 ---
 .../genotype_plink/hue_geno_3455_accessions.hapmap.plk.bed     | 3 ---
 .../genotype_plink/hue_geno_3455_accessions.hapmap.plk.bim     | 3 ---
 .../genotype_plink/hue_geno_3455_accessions.hapmap.plk.fam     | 3 ---
 .../genotype_plink/hue_geno_3455_accessions.hapmap.plk.log     | 3 ---
 .../genotype_plink/hue_geno_3455_accessions.hapmap.plk.map     | 3 ---
 .../genotype_plink/hue_geno_3455_accessions.hapmap.plk.nosex   | 3 ---
 .../genotype_plink/hue_geno_3455_accessions.hapmap.plk.ped     | 3 ---
 .../genotype_plink/lux_geno_3455_accessions.hapmap.plk.bed     | 3 ---
 .../genotype_plink/lux_geno_3455_accessions.hapmap.plk.bim     | 3 ---
 .../genotype_plink/lux_geno_3455_accessions.hapmap.plk.fam     | 3 ---
 .../genotype_plink/lux_geno_3455_accessions.hapmap.plk.log     | 3 ---
 .../genotype_plink/lux_geno_3455_accessions.hapmap.plk.map     | 3 ---
 .../genotype_plink/lux_geno_3455_accessions.hapmap.plk.nosex   | 3 ---
 .../genotype_plink/lux_geno_3455_accessions.hapmap.plk.ped     | 3 ---
 .../genotype_plink/make_bed_4rm_tassel_plink_outputs.sh        | 3 ---
 .../mex_chalco_geno_3455_accessions.hapmap.plk.bed             | 3 ---
 .../mex_chalco_geno_3455_accessions.hapmap.plk.bim             | 3 ---
 .../mex_chalco_geno_3455_accessions.hapmap.plk.fam             | 3 ---
 .../mex_chalco_geno_3455_accessions.hapmap.plk.log             | 3 ---
 .../mex_chalco_geno_3455_accessions.hapmap.plk.map             | 3 ---
 .../mex_chalco_geno_3455_accessions.hapmap.plk.nosex           | 3 ---
 .../mex_chalco_geno_3455_accessions.hapmap.plk.ped             | 3 ---
 .../mex_durango_geno_3455_accessions.hapmap.plk.bed            | 3 ---
 .../mex_durango_geno_3455_accessions.hapmap.plk.bim            | 3 ---
 .../mex_durango_geno_3455_accessions.hapmap.plk.fam            | 3 ---
 .../mex_durango_geno_3455_accessions.hapmap.plk.log            | 3 ---
 .../mex_durango_geno_3455_accessions.hapmap.plk.map            | 3 ---
 .../mex_durango_geno_3455_accessions.hapmap.plk.nosex          | 3 ---
 .../mex_durango_geno_3455_accessions.hapmap.plk.ped            | 3 ---
 .../genotype_plink/mex_geno_3455_accessions.hapmap.plk.bed     | 3 ---
 .../genotype_plink/mex_geno_3455_accessions.hapmap.plk.bim     | 3 ---
 .../genotype_plink/mex_geno_3455_accessions.hapmap.plk.fam     | 3 ---
 .../genotype_plink/mex_geno_3455_accessions.hapmap.plk.log     | 3 ---
 .../genotype_plink/mex_geno_3455_accessions.hapmap.plk.map     | 3 ---
 .../genotype_plink/mex_geno_3455_accessions.hapmap.plk.nosex   | 3 ---
 .../genotype_plink/mex_geno_3455_accessions.hapmap.plk.ped     | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.plk.bed       | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.plk.bim       | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.plk.fam       | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.plk.log       | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.plk.map       | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.plk.nosex     | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.plk.ped       | 3 ---
 .../mex_nobogame_geno_3455_accessions.hapmap.plk.bed           | 3 ---
 .../mex_nobogame_geno_3455_accessions.hapmap.plk.bim           | 3 ---
 .../mex_nobogame_geno_3455_accessions.hapmap.plk.fam           | 3 ---
 .../mex_nobogame_geno_3455_accessions.hapmap.plk.log           | 3 ---
 .../mex_nobogame_geno_3455_accessions.hapmap.plk.map           | 3 ---
 .../mex_nobogame_geno_3455_accessions.hapmap.plk.nosex         | 3 ---
 .../mex_nobogame_geno_3455_accessions.hapmap.plk.ped           | 3 ---
 .../genotype_plink/nica_geno_3455_accessions.hapmap.plk.bed    | 3 ---
 .../genotype_plink/nica_geno_3455_accessions.hapmap.plk.bim    | 3 ---
 .../genotype_plink/nica_geno_3455_accessions.hapmap.plk.fam    | 3 ---
 .../genotype_plink/nica_geno_3455_accessions.hapmap.plk.log    | 3 ---
 .../genotype_plink/nica_geno_3455_accessions.hapmap.plk.map    | 3 ---
 .../genotype_plink/nica_geno_3455_accessions.hapmap.plk.nosex  | 3 ---
 .../genotype_plink/nica_geno_3455_accessions.hapmap.plk.ped    | 3 ---
 .../genotype_plink/parv_geno_3455_accessions.hapmap.plk.bed    | 3 ---
 .../genotype_plink/parv_geno_3455_accessions.hapmap.plk.bim    | 3 ---
 .../genotype_plink/parv_geno_3455_accessions.hapmap.plk.fam    | 3 ---
 .../genotype_plink/parv_geno_3455_accessions.hapmap.plk.log    | 3 ---
 .../genotype_plink/parv_geno_3455_accessions.hapmap.plk.map    | 3 ---
 .../genotype_plink/parv_geno_3455_accessions.hapmap.plk.nosex  | 3 ---
 .../genotype_plink/parv_geno_3455_accessions.hapmap.plk.ped    | 3 ---
 .../parv_geno_3455_accessions.hapmap.plk.ped_orginal           | 3 ---
 ...eno_3455_accessions.hapmap.plk.ped_tabs_replaced_with_space | 3 ---
 .../genotype_plink/per_geno_3455_accessions.hapmap.plk.bed     | 3 ---
 .../genotype_plink/per_geno_3455_accessions.hapmap.plk.bim     | 3 ---
 .../genotype_plink/per_geno_3455_accessions.hapmap.plk.fam     | 3 ---
 .../genotype_plink/per_geno_3455_accessions.hapmap.plk.log     | 3 ---
 .../genotype_plink/per_geno_3455_accessions.hapmap.plk.map     | 3 ---
 .../genotype_plink/per_geno_3455_accessions.hapmap.plk.nosex   | 3 ---
 .../genotype_plink/per_geno_3455_accessions.hapmap.plk.ped     | 3 ---
 .../gwas_data_3455_accessions/genotype_vcf/README.md           | 3 ---
 .../genotype_vcf/all_taxa_3455_accessions.hapmap.vcf           | 3 ---
 .../genotype_vcf/all_taxa_3455_accessions.hapmap.vcf.gz        | 3 ---
 .../genotype_vcf/all_taxa_3455_accessions.hapmap.vcf.gz.tbi    | 3 ---
 .../genotype_vcf/diplo_per_geno_3455_accessions.hapmap.vcf     | 3 ---
 .../genotype_vcf/hue_geno_3455_accessions.hapmap.vcf           | 3 ---
 .../genotype_vcf/lux_geno_3455_accessions.hapmap.vcf           | 3 ---
 .../genotype_vcf/mex_chalco_geno_3455_accessions.hapmap.vcf    | 3 ---
 .../genotype_vcf/mex_durango_geno_3455_accessions.hapmap.vcf   | 3 ---
 .../genotype_vcf/mex_geno_3455_accessions.hapmap.vcf           | 3 ---
 .../mex_mesa_central_geno_3455_accessions.hapmap.vcf           | 3 ---
 .../genotype_vcf/mex_nobogame_geno_3455_accessions.hapmap.vcf  | 3 ---
 .../genotype_vcf/nica_geno_3455_accessions.hapmap.vcf          | 3 ---
 .../genotype_vcf/parv_geno_3455_accessions.hapmap.vcf          | 3 ---
 .../genotype_vcf/per_geno_3455_accessions.hapmap.vcf           | 3 ---
 .../phenotype/all_taxa_3455_accessions.csv                     | 3 ---
 .../phenotype/all_taxa_pheno_3455_accessions.csv               | 3 ---
 .../phenotype/diplo_per_pheno_3455_accessions.csv              | 3 ---
 .../phenotype/diplo_plus_perennis_pheno_3455_accessions.csv    | 3 ---
 .../phenotype/hue_pheno_3455_accessions.csv                    | 3 ---
 .../phenotype/lux_pheno_3455_accessions.csv                    | 3 ---
 .../phenotype/lux_plus_nica_pheno_3455_accessions.csv          | 3 ---
 .../phenotype/mex_chalco_pheno_3455_accessions.csv             | 3 ---
 .../phenotype/mex_durango_pheno_3455_accessions.csv            | 3 ---
 .../phenotype/mex_mesa_central_pheno_3455_accessions.csv       | 3 ---
 .../phenotype/mex_nobogame_pheno_3455_accessions.csv           | 3 ---
 .../phenotype/mex_pheno_3455_accessions.csv                    | 3 ---
 .../phenotype/nica_pheno_3455_accessions.csv                   | 3 ---
 .../phenotype/parv_pheno_3455_accessions.csv                   | 3 ---
 .../phenotype/parv_plus_hue_pheno_3455_accessions.csv          | 3 ---
 .../phenotype/per_pheno_3455_accessions.csv                    | 3 ---
 .../phenotype/plink_fomart/.fuse_hidden000a6cf200000003        | 3 ---
 .../phenotype/plink_fomart/all_taxa_pheno_plink.txt            | 3 ---
 .../phenotype/plink_fomart/diplo_per_pheno_plink.txt           | 3 ---
 .../phenotype/plink_fomart/hue_pheno.csv                       | 3 ---
 .../phenotype/plink_fomart/hue_pheno_plink.csv                 | 3 ---
 .../phenotype/plink_fomart/hue_pheno_plink.log                 | 3 ---
 .../phenotype/plink_fomart/hue_pheno_plink.txt                 | 3 ---
 .../phenotype/plink_fomart/lux_pheno_plink.txt                 | 3 ---
 .../phenotype/plink_fomart/mex_chalco_pheno_plink.txt          | 3 ---
 .../phenotype/plink_fomart/mex_durango_pheno_plink.txt         | 3 ---
 .../phenotype/plink_fomart/mex_mesa_central_pheno_plink.txt    | 3 ---
 .../phenotype/plink_fomart/mex_nobogame_pheno_plink.txt        | 3 ---
 .../phenotype/plink_fomart/mex_pheno_plink.txt                 | 3 ---
 .../phenotype/plink_fomart/nica_pheno_plink.txt                | 3 ---
 .../phenotype/plink_fomart/parv_pheno.csv                      | 3 ---
 .../phenotype/plink_fomart/parv_pheno_plink.txt                | 3 ---
 .../phenotype/plink_fomart/per_pheno_plink.txt                 | 3 ---
 235 files changed, 702 deletions(-)
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/README.md
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/all_taxa_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/diplo_per_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/diplo_plus_perennis_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/hue_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/lux_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/lux_plus_nica_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/mex_chalco_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/mex_durango_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/mex_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/mex_hapmap_101.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/mex_mesa_central_geno_3455_accessions.hapmap.txt
 delete mode 100644 studies/processed_genotype_phenotype_teosinte_data/gwas_data_3455_accessions/genotype/mex_nobogame_geno_3455_accessions.hapmap.txt
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GitLab