available for hackingenhancementgood first issue
Métriques du dépôt
- Stars
- (1 217 stars)
- Métriques de merge PR
- (Merge moyen 2j 12h) (4 PRs mergées en 30 j)
Description
janitor.biology could do with a to_fasta function, I think. The intent here would be to conveniently export a dataframe of sequences as a FASTA file, using one column as the fasta header.
strawman implementation below:
import pandas_flavor as pf
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from Bio import SeqIO
@pf.register_dataframe_method
def to_fasta(df, identifier_column_name, sequence_column_name, filename):
seq_records = []
for r, d in df.iterrows():
seq = Seq(d[sequence_column_name])
seq_record = SeqRecord(seq, id=d[identifier_column_name], description="", name="")
seq_records.append(seq_record)
SeqIO.write(seq_records, filename, format="fasta")