https://github.com/pgarrett-scripps/fastaframes
Python package to convert between FASTA files and Pandas DataFrames.
https://github.com/pgarrett-scripps/fastaframes
bioinformatics fasta mass-spectrometry package pandas protein protein-sequences proteomics python
Last synced: 3 months ago
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Python package to convert between FASTA files and Pandas DataFrames.
- Host: GitHub
- URL: https://github.com/pgarrett-scripps/fastaframes
- Owner: pgarrett-scripps
- License: mit
- Created: 2023-05-02T03:12:44.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-10-04T00:33:27.000Z (about 2 years ago)
- Last Synced: 2024-11-08T06:43:34.965Z (11 months ago)
- Topics: bioinformatics, fasta, mass-spectrometry, package, pandas, protein, protein-sequences, proteomics, python
- Language: Python
- Homepage:
- Size: 43 KB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# FastaFrames
FastaFrames is a python package to convert between FASTA files and pandas DataFrames.
## Usage
To install fastaframes use pip:
```sh
pip install fastaframes
```
### Reading a FASTA file
```python
from fastaframes import to_df
fasta_df = to_df(data='example.fasta')
```
### Writing a FASTA file
```python
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 |