reduce sniffer data content

tdayris · Jan 16, 2024 · 720e4c2 · 720e4c2
1 parent 8a3cb2f
commit 720e4c2
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,10 @@
 * Snakemake-wrappers up to 3.3.3
 * Snakemake 8+ compatibility
 
+## Fix:
+
+* csv.Sniffer getting too much data
+
 # 2.2.7
 
 ## Features:

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -23,7 +23,7 @@ snakemake.utils.validate(config, "../schemas/config.schema.yaml")
 # Load and check samples properties table
 sample_table_path: str = config.get("samples", "config/samples.csv")
 with open(sample_table_path, "r") as sample_table_stream:
-    dialect: csv.Dialect = csv.Sniffer().sniff(sample_table_stream.read(1024))
+    dialect: csv.Dialect = csv.Sniffer().sniff(sample_table_stream.readline())
     sample_table_stream.seek(0)
 
 samples: pandas.DataFrame = pandas.read_csv(
@@ -41,7 +41,7 @@ snakemake.utils.validate(samples, "../schemas/samples.schema.yaml")
 genome_table_path: str = config.get("genomes")
 if genome_table_path:
     with open(genome_table_path, "r") as genome_table_stream:
-        dialect: csv.Dialect = csv.Sniffer().sniff(genome_table_stream.read(1024))
+        dialect: csv.Dialect = csv.Sniffer().sniff(genome_table_stream.readline())
         genome_table_stream.seek(0)
 
     genomes: pandas.DataFrame = pandas.read_csv(