pyjanitor-devs/pyjanitor

[ENH] to_fasta as part of janitor.biology

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#646 opened on Mar 12, 2020

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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")

Contributor guide

Research direction
Implement the to fasta function as described in the issue body, using pandas flavor to register it as a DataFrame method. Ensure proper import of Bio.Seq, Bio.SeqRecord, and Bio.SeqIO. Write tests to verify output FASTA format.
Tech stack
python
Domain
backend
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
PythonpandasBioPython
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
80