A very simple fasta file parser.
Project description
FastaFrames
FastaFrames is a python package to convert between FASTA files and pandas DataFrames.
Usage
To install fastaframes use pip:
pip install fastaframes
Reading a FASTA file
from fastaframes import to_df
fasta_df = to_df(data='example.fasta')
Writing a FASTA file
from fastaframes import to_fasta
to_fasta(data=fasta_df, output_file='output.fasta')
Columns:
- db: Database from which the sequence was retrieved. db is 'sp' for UniProtKB/Swiss-Prot and 'tr' for UniProtKB/TrEMBL.
- unique_identifier: The primary accession number of the UniProtKB entry.
- entry_name: The entry name of the UniProtKB entry.
- protein_name: The recommended name of the UniProtKB entry as annotated in the RecName field. For UniProtKB/TrEMBL entries without a RecName field, the SubName field is used. In case of multiple SubNames, the first one is used. The 'precursor' attribute is excluded, 'Fragment' is included with the name if applicable.
- organism_name: The scientific name of the organism of the UniProtKB entry.
- organism_identifier: The unique identifier of the source organism, assigned by the NCBI.
- gene_name: The first gene name of the UniProtKB entry. If there is no gene name, OrderedLocusName or ORFname, the GN field is not listed.
- protein_existence: The numerical value describing the evidence for the existence of the protein.
- sequence_version: The version number of the sequence.
- protein_sequence: The protein amino acid sequence.
Example FASTA file:
>sp|A0A087X1C5|CP2D7_HUMAN Putative cytochrome P450 2D7 OS=Homo sapiens OX=9606 GN=CYP2D7 PE=5 SV=1
MGLEALVPLAMIVAIFLLLVDLMHRHQRWAARYPPGPLPLPGLGNLLHVDFQNTPYCFDQ
Will produce the following:
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 |
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