correct SyntaxWarning

jaleezyy · Mar 24, 2024 · 5cbc18d · 5cbc18d
1 parent 2106195
commit 5cbc18d
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/Snakefile b/Snakefile
@@ -649,7 +649,7 @@ rule run_freebayes:
         # apply ambiguous variants first using IUPAC codes. this variant set cannot contain indels or the subsequent step will break
         bcftools consensus -f {input.reference} -I {params.out}.ambiguous.norm.vcf.gz > {params.out}.ambiguous.fasta 
         # apply remaninng variants, including indels
-        bcftools consensus -f {params.out}.ambiguous.fasta -m {params.out}.mask.txt {params.out}.fixed.norm.vcf.gz | sed s/MN908947\.3.*/{wildcards.sn}/ > {output.consensus}
+        bcftools consensus -f {params.out}.ambiguous.fasta -m {params.out}.mask.txt {params.out}.fixed.norm.vcf.gz | sed s/MN908947\\.3.*/{wildcards.sn}/ > {output.consensus}
         """
 
 rule consensus_compare:

diff --git a/scripts/signal_postprocess.py b/scripts/signal_postprocess.py
@@ -649,7 +649,7 @@ def parse_lineage(tsv_filename, sample_names, allow_missing=True):
     # Pull each row, identify sid 
     for row in df.itertuples():
         if row.isolate.startswith("Consensus"):
-            sid = re.findall("_(.*?)\.", row.isolate)[0]
+            sid = re.findall(r"_(.*?)\.", row.isolate)[0]
         else:
             sid = str(row.isolate)