From a6fece918d652ad220432fac8b08c02a6a3ad73a Mon Sep 17 00:00:00 2001 From: Karan Jaisingh Date: Thu, 9 Jan 2025 11:50:13 -0500 Subject: [PATCH] Reordered PED file columns when creating --- scripts/notebooks/SampleQC.ipynb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/notebooks/SampleQC.ipynb b/scripts/notebooks/SampleQC.ipynb index 91d83a196..8901311f1 100644 --- a/scripts/notebooks/SampleQC.ipynb +++ b/scripts/notebooks/SampleQC.ipynb @@ -1402,9 +1402,9 @@ " reference_ped[\"Phenotype\"] = \"0\"\n", " \n", " # Assign sexes based on sex assignment dictionary\n", - " computed_ped = reference_ped[['Sample_ID', 'Family_ID', 'Paternal_ID', 'Maternal_ID', 'Phenotype']]\n", + " computed_ped = reference_ped[['Family_ID', 'Sample_ID', 'Paternal_ID', 'Maternal_ID', 'Phenotype']]\n", " computed_ped['Sex'] = computed_ped['Sample_ID'].map(sex_assignments).map(SEX_CODES)\n", - " computed_ped = computed_ped[['Sample_ID', 'Family_ID', 'Paternal_ID', 'Maternal_ID', 'Sex', 'Phenotype']]\n", + " computed_ped = computed_ped[['Family_ID', 'Sample_ID', 'Paternal_ID', 'Maternal_ID', 'Sex', 'Phenotype']]\n", " computed_ped = computed_ped[computed_ped['Sample_ID'].isin(sex_assignments.keys())]\n", " \n", " # Save dataframe\n", @@ -2715,7 +2715,7 @@ "file_path = generate_file_path(TLD_PATH, 'sex_analysis', 'sample_qc.ped')\n", "create_ped(updated_sex, reference_ped, file_path)\n", "\n", - "created_ped = pd.read_table(file_path, names=['Sample_ID', 'Family_ID', 'Paternal_ID', \n", + "created_ped = pd.read_table(file_path, names=['Family_ID', 'Sample_ID', 'Paternal_ID',\n", " 'Maternal_ID', 'Sex', 'Phenotype'])\n", "created_ped" ]