Cookbook¶
Merge two sequence files¶
Use pandas.concat
to merge two sequence files.
import phylopandas as ph
seq1 = ph.read_fasta('seq1.fasta')
seq2 = ph.read_fasta('seq2.fasta')
# Merge two files
seqs = seq1.concat(seq2, ignore_index=False)
# Write to file.
seqs.to_fasta('seqs.fasta')
Merge alignment and sequence data¶
Add alignment column to sequence DataFrame.
import phylopandas as ph
# Read sequences and alignments.
seq = ph.read_fasta('sequences.fasta')
ali = ph.read_fasta('alignment.fasta')
# Merge data.
seq.merge(ali, on='id')