From 69ced2dcbfc997e792472c946bcb5558b1a5c997 Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Thu, 2 May 2019 14:22:10 +0200
Subject: [PATCH] 1000RNASeq_chicken_calling : pandas read_table deprecated,
use read_csv with sep='\t'
---
Snakemake/1000RNASeq_chicken/calling/Snakefile_calling | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakemake/1000RNASeq_chicken/calling/Snakefile_calling b/Snakemake/1000RNASeq_chicken/calling/Snakefile_calling
index 2c59095..7e8e72a 100644
--- a/Snakemake/1000RNASeq_chicken/calling/Snakefile_calling
+++ b/Snakemake/1000RNASeq_chicken/calling/Snakefile_calling
@@ -32,7 +32,7 @@ if "bin_dir" in config:
os.environ['PATH'] = config["bin_dir"] + os.pathsep + os.environ['PATH']
# sample config
-table = pd.read_table(config["sample_config"], dtype=str)
+table = pd.read_csv(config["sample_config"], dtype=str,sep='\t')
available_PL=["ILLUMINA","SLX","SOLEXA","SOLID","454","LS454","COMPLETE","PACBIO","IONTORRENT","CAPILLARY","HELICOS","UNKNOWN"]
sequencer=table.sequencer.unique()
--
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