fastaframes 0.0.2

A very simple fasta file parser.

FastaFrames

This Python module provides a set of functions to work with FASTA files. It allows you to read FASTA files, convert them to pandas dataframes, manipulate data, and write data back to FASTA files. It also supports converting FASTA files to a list of FastaEntry dataclass objects.

Features

• Read FASTA files into pandas DataFrames
• Write FASTA files from pandas DataFrames

Usage

To install fastaframes use pip:

pip install fastaframes

Reading FASTA files

To read a FASTA file and convert it to a pandas DataFrame:

from fastaframes import to_df

# IO input
with open('example.fasta', 'r') as fasta_io:
    fasta_df = to_df(fasta_data=fasta_io)

# or

# File input
fasta_df = to_df(fasta_data='example.fasta')
    
print(fasta_df.head())

Writing FASTA files

To write a pandas DataFrame to a FASTA file:

from fastaframes import to_fasta

# Write StringIO to file
fasta_io = to_fasta(fasta_data=fasta_df) # outputs StringIO if file=None
with open('output.fasta', 'w') as output_file:
    output_file.write(fasta_io.getvalue())

# or
    
# Write directly to file
to_fasta(fasta_data=fasta_df, file='output.fasta')

Example DataFrame:

	db	unique_identifier	entry_name	protein_name	organism_name	organism_identifier	gene_name	protein_existence	sequence_version	protein_sequence
0	sp	A0A087X1C5	CP2D7_HUMAN	Putative cytochrome P450 2D7	Homo sapiens	9606.0	CYP2D7	5.0	1.0	MGLEALVPLAMIVAIFLLLVDLMHRHQRWAARYPPGPLPLPGLGNLLHVDFQNTPYCFDQ
1	sp	A0A0B4J2F2	SIK1B_HUMAN	Putative serine/threonine-protein kinase SIK1B	Homo sapiens	9606.0	SIK1B	5.0	1.0	MVIMSEFSADPAGQGQGQQKPLRVGFYDIERTLGKGNFAVVKLARHRVTKTQVAIKIIDKLVQ
2	sp	A0A0C5B5G6	MOTSC_HUMAN	Mitochondrial-derived peptide MOTS-c	Homo sapiens	9606.0	MT-RNR1	1.0	1.0	MRWQEMGYIFYPRKLR
3	sp	A0A0K2S4Q6	CD3CH_HUMAN	Protein CD300H	Homo sapiens	9606.0	CD300H	1.0	1.0	MTQRAGAAMLPSALLLLCVPGCLTVSGPSTVMGAVGESLSVQCRYEEKYKTFNKYWCRQP