From ac389edebb7e49bed3a7d2d24ba3a0f8882ba490 Mon Sep 17 00:00:00 2001 From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr> Date: Tue, 3 Mar 2020 16:48:41 +0100 Subject: [PATCH] src/db_utils/config.py: modification of prefixes gin to cin in Config.table + creation of Config.bed_exon and Config.bed_gene variable --- src/db_utils/config.py | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/src/db_utils/config.py b/src/db_utils/config.py index ed768dad..107f80ff 100755 --- a/src/db_utils/config.py +++ b/src/db_utils/config.py @@ -17,13 +17,15 @@ class Config: A class containing every parameters used in the submodule db_utils """ db_file = Path(__file__).parents[2] / "results" / 'chia_pet_database.db' - tables = ["gin_gene", "gin_exon", "gin_frequency", "gin_interaction"] - bed_orf = Path(__file__).parents[1] / "data" / "exon_orf.bed" - bed_exon = Path(__file__).parents[1] / "data" / "exon_freq.bed" - output = Path(__file__).parents[2] / "results" - exon_intern = Path(__file__).parents[1] / "data" / "exon_intern.bed" - ctrl_exon_file = output / "CTRL_exons.txt" - exon_file = output / "exons.txt" - gene_file = Path(__file__).parents[1] / "data" / "genes.csv" - frequency_file = output / "frequency.txt" + tables = ["cin_gene", "cin_exon", "cin_frequency", "cin_interaction"] + bed_exon = Path(__file__).parents[2] / 'data' / 'bed' / 'exon.bed' + bed_gene = Path(__file__).parents[2] / 'data' / 'bed' / 'gene.bed' + # bed_orf = Path(__file__).parents[1] / "data" / "exon_orf.bed" + # bed_exon_freq = Path(__file__).parents[1] / "data" / "exon_freq.bed" + # output = Path(__file__).parents[2] / "results" + # exon_intern = Path(__file__).parents[1] / "data" / "exon_intern.bed" + # ctrl_exon_file = output / "CTRL_exons.txt" + # exon_file = output / "exons.txt" + # gene_file = Path(__file__).parents[1] / "data" / "genes.csv" + # frequency_file = output / "frequency.txt" -- GitLab