From 2c8a35b421b0e5590fd3aebec4d9eafc49c0bdb6 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Tue, 17 Sep 2024 17:12:31 +0200 Subject: [PATCH] :bug: fix sample metadata Deal with scientific name for some goat samples --- Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index 0598120..ed0b0c3 100644 --- a/Makefile +++ b/Makefile @@ -425,13 +425,13 @@ data: requirements --dataset SMARTER_CHFR.zip --chip_name IlluminaGoatSNP50 --assembly $(ASSEMBLY) --create_samples;) $(PYTHON_INTERPRETER) src/data/import_samples.py --src_dataset burren_et_al_2016.zip \ --datafile doi_10.5061_dryad.q1cv6__v1/burren_samples_fix.xlsx --code_column code --id_column original_id \ - --chip_name IlluminaGoatSNP50 --country_all Switzerland --species_all Goat --alias_column alias + --chip_name IlluminaGoatSNP50 --country_all Switzerland --species_all "Capra hircus" --alias_column alias $(PYTHON_INTERPRETER) src/data/import_samples.py --src_dataset cortellari_et_al_2021.zip \ --datafile s41598-021-89900-2/cortellari_samples_fix.xlsx --code_column fid --id_column original_id \ - --chip_name IlluminaGoatSNP50 --country_all Italy --species_all Goat + --chip_name IlluminaGoatSNP50 --country_all Italy --species_all "Capra hircus" $(PYTHON_INTERPRETER) src/data/import_samples.py --src_dataset Guisandesa.zip \ --datafile Guisandesa/Guisandesa.xlsx --code_all GUI --id_column original_id \ - --chip_name AffymetrixAxiomGoatv2 --country_all Spain --species_all Goat + --chip_name AffymetrixAxiomGoatv2 --country_all Spain --species_all "Capra hircus" ## convert genotypes without creating samples in database (GOAT) $(foreach ASSEMBLY, $(GOAT_ASSEMBLIES), $(PYTHON_INTERPRETER) src/data/import_from_plink.py --bfile ADAPTmap_genotypeTOP_20161201/binary_fileset/ADAPTmap_genotypeTOP_20161201 \