From 3f736ca966b5582075ff090c6133d6135a5aa730 Mon Sep 17 00:00:00 2001 From: Belen Otero Carrasco Date: Tue, 20 Dec 2022 11:23:43 +0100 Subject: [PATCH] processed data --- ...get gene-based treated disease_CSBJ_DREBIOP.ipynb | 12 ++++++------ ...t gene-based treated disease_REPODB_DREBIOP.ipynb | 12 ++++++------ .../Processed data/2. Processed data DREGE.ipynb | 12 ++++++------ ...rget gene-based treated disease _CSBJ-DREGE.ipynb | 8 ++++---- ...get gene-based treated disease_REPODB-DREGE.ipynb | 8 ++++---- 5 files changed, 26 insertions(+), 26 deletions(-) diff --git a/Notebooks/Processed data/1.1 Target gene-based treated disease_CSBJ_DREBIOP.ipynb b/Notebooks/Processed data/1.1 Target gene-based treated disease_CSBJ_DREBIOP.ipynb index 0b4a24a..e336c60 100644 --- a/Notebooks/Processed data/1.1 Target gene-based treated disease_CSBJ_DREBIOP.ipynb +++ b/Notebooks/Processed data/1.1 Target gene-based treated disease_CSBJ_DREBIOP.ipynb @@ -29,7 +29,7 @@ "metadata": {}, "outputs": [], "source": [ - "cases_csbj = pd.read_csv(\"final_cases_csbj.tsv\", sep='\\t')\n", + "cases_csbj = pd.read_csv(\"./Data/Input/DISNET/final_cases_csbj.tsv\", sep='\\t')\n", "cases_csbj = cases_csbj.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -39,7 +39,7 @@ "metadata": {}, "outputs": [], "source": [ - "triplets_csbj = pd.read_excel(\"triplets_chembl_disnet.xlsx\",engine='openpyxl')\n", + "triplets_csbj = pd.read_excel(\"./Data/Input/DISNET/triplets_chembl_disnet.xlsx\",engine='openpyxl')\n", "triplets_csbj =triplets_csbj.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -101,7 +101,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", + "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n", "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -120,7 +120,7 @@ "metadata": {}, "outputs": [], "source": [ - "drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", + "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n", "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -171,7 +171,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_path_direct = pd.read_csv('disease_pathway.tsv', sep='\\t')" + "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')" ] }, { @@ -196,7 +196,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen_pw = pd.read_csv('dis_gen_pw.tsv', sep='\\t')\n", + "dis_gen_pw = pd.read_csv('./Data/Input/DISNET/dis_gen_pw.tsv', sep='\\t')\n", "dis_gen_pw = dis_gen_pw.drop([\"Unnamed: 0\"],axis=1)" ] }, diff --git a/Notebooks/Processed data/1.2 Target gene-based treated disease_REPODB_DREBIOP.ipynb b/Notebooks/Processed data/1.2 Target gene-based treated disease_REPODB_DREBIOP.ipynb index 44fb320..cad2ae0 100644 --- a/Notebooks/Processed data/1.2 Target gene-based treated disease_REPODB_DREBIOP.ipynb +++ b/Notebooks/Processed data/1.2 Target gene-based treated disease_REPODB_DREBIOP.ipynb @@ -29,7 +29,7 @@ "metadata": {}, "outputs": [], "source": [ - "cases_repodb = pd.read_csv(\"final_cases_repodb.tsv\", sep='\\t')" + "cases_repodb = pd.read_csv(\"./Data/Input/DISNET/final_cases_repodb.tsv\", sep='\\t')" ] }, { @@ -47,7 +47,7 @@ "metadata": {}, "outputs": [], "source": [ - "triplets_repodb = pd.read_csv('repodb_all_triples.tsv', sep='\\t')" + "triplets_repodb = pd.read_csv('./Data/Input/DISNET/repodb_all_triples.tsv', sep='\\t')" ] }, { @@ -144,7 +144,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", + "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n", "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -183,7 +183,7 @@ "metadata": {}, "outputs": [], "source": [ - "drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", + "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n", "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -339,7 +339,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_path_direct = pd.read_csv('disease_pathway.tsv', sep='\\t')" + "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')" ] }, { @@ -483,7 +483,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen_pw = pd.read_csv('dis_gen_pw.tsv', sep='\\t')\n", + "dis_gen_pw = pd.read_csv('./Data/Input/DISNET/dis_gen_pw.tsv', sep='\\t')\n", "dis_gen_pw = dis_gen_pw.drop([\"Unnamed: 0\"],axis=1)" ] }, diff --git a/Notebooks/Processed data/2. Processed data DREGE.ipynb b/Notebooks/Processed data/2. Processed data DREGE.ipynb index 9796099..680a6dd 100644 --- a/Notebooks/Processed data/2. Processed data DREGE.ipynb +++ b/Notebooks/Processed data/2. Processed data DREGE.ipynb @@ -29,7 +29,7 @@ "metadata": {}, "outputs": [], "source": [ - "duples_repodb = pd.read_csv(\"repoDB_all_disdru.tsv\", sep='\\t')" + "duples_repodb = pd.read_csv(\"./Data/Input/Drug Repurposing/repoDB_all_disdru.tsv\", sep='\\t')" ] }, { @@ -38,7 +38,7 @@ "metadata": {}, "outputs": [], "source": [ - "duples_csbj = pd.read_csv(\"duplas_CSBJ.tsv\")" + "duples_csbj = pd.read_csv(\"./Data/Input/Drug Repurposing/duplas_CSBJ.tsv\")" ] }, { @@ -173,7 +173,7 @@ } ], "source": [ - "dis_path_direct = pd.read_csv('disease_pathway.tsv', sep='\\t')\n", + "dis_path_direct = pd.read_csv('./Data/Input/DISNET/disease_pathway.tsv', sep='\\t')\n", "dis_path_direct" ] }, @@ -183,7 +183,7 @@ "metadata": {}, "outputs": [], "source": [ - "drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')" + "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')" ] }, { @@ -201,7 +201,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen = pd.read_csv('dis_genes_gda.tsv', sep='\\t')" + "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes_gda.tsv', sep='\\t')" ] }, { @@ -219,7 +219,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen_sinfil = pd.read_csv('dis_genes.tsv', sep='\\t')" + "dis_gen_sinfil = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')" ] }, { diff --git a/Notebooks/Processed data/2.1 Target gene-based treated disease _CSBJ-DREGE.ipynb b/Notebooks/Processed data/2.1 Target gene-based treated disease _CSBJ-DREGE.ipynb index 557ae98..10d104d 100644 --- a/Notebooks/Processed data/2.1 Target gene-based treated disease _CSBJ-DREGE.ipynb +++ b/Notebooks/Processed data/2.1 Target gene-based treated disease _CSBJ-DREGE.ipynb @@ -29,7 +29,7 @@ "metadata": {}, "outputs": [], "source": [ - "cases_csbj_target = pd.read_csv(\"cases_csbj_target.tsv\", sep =\"\\t\")\n", + "cases_csbj_target = pd.read_csv(\"./Data/Input/DISNET/cases_csbj_target.tsv\", sep =\"\\t\")\n", "cases_csbj = cases_csbj_target.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -59,7 +59,7 @@ "metadata": {}, "outputs": [], "source": [ - "triplets_csbj = pd.read_excel(\"triplets_chembl_disnet.xlsx\",engine='openpyxl')" + "triplets_csbj = pd.read_excel(\"./Data/Input/DISNET/triplets_chembl_disnet.xlsx\",engine='openpyxl')" ] }, { @@ -167,7 +167,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", + "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n", "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -186,7 +186,7 @@ "metadata": {}, "outputs": [], "source": [ - "drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", + "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n", "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, diff --git a/Notebooks/Processed data/2.2 Target gene-based treated disease_REPODB-DREGE.ipynb b/Notebooks/Processed data/2.2 Target gene-based treated disease_REPODB-DREGE.ipynb index 5cde080..f561b5e 100644 --- a/Notebooks/Processed data/2.2 Target gene-based treated disease_REPODB-DREGE.ipynb +++ b/Notebooks/Processed data/2.2 Target gene-based treated disease_REPODB-DREGE.ipynb @@ -29,7 +29,7 @@ "metadata": {}, "outputs": [], "source": [ - "cases_repodb = pd.read_csv(\"cases_repodb_target.tsv\", sep='\\t')\n", + "cases_repodb = pd.read_csv(\"./Data/Input/DISNET/cases_repodb_target.tsv\", sep='\\t')\n", "cases_repodb = cases_repodb.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -59,7 +59,7 @@ "metadata": {}, "outputs": [], "source": [ - "triplets_repodb = pd.read_csv('repodb_all_triples.tsv', sep='\\t')" + "triplets_repodb = pd.read_csv('./Data/Input/DISNET/repodb_all_triples.tsv', sep='\\t')" ] }, { @@ -236,7 +236,7 @@ "metadata": {}, "outputs": [], "source": [ - "dis_gen = pd.read_csv('dis_genes.tsv', sep='\\t')\n", + "dis_gen = pd.read_csv('./Data/Input/DISNET/dis_genes.tsv', sep='\\t')\n", "dis_gen = dis_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, @@ -275,7 +275,7 @@ "metadata": {}, "outputs": [], "source": [ - "drug_gen = pd.read_csv('drug_gen.tsv', sep='\\t')\n", + "drug_gen = pd.read_csv('./Data/Input/DISNET/drug_gen.tsv', sep='\\t')\n", "drug_gen = drug_gen.drop([\"Unnamed: 0\"],axis=1)" ] }, -- 2.24.1