fix: fix syntax errors
@@ -53,10 +53,10 @@ rule extract_meta:
from Bio import SeqIO
import pandas as pd
- seq_names = [s.id for s in SeqIO.read(input.alignment, 'fasta')]
+ seq_names = [s.id for s in SeqIO.parse(input.alignment, 'fasta')]
all_meta = pd.read_csv(input.metadata, sep='\t', index_col=0)
- extracted_meta = meta.loc[seq_names]
- extract_meta.to_csv(output.metadata, sep='\t')
+ extracted_meta = all_meta.loc[seq_names]
+ extracted_meta.to_csv(output.metadata, sep='\t')
# Allows 'normal' run of export to be forced to correct lat-long & ordering
