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A lightweight Python module to read and write FASTA sequence records

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# fastapy
A lightweight Python package to read and write sequence records in [FASTA format](https://en.wikipedia.org/wiki/FASTA_format).

The design was inspired by the utility of BioPython’s SeqIO, which supports many sequence formats. This repo focuses only on FASTA records. It is faster than BioPython, can handle compressed FASTA files (gzip, bzip2, zip), and has no Python package dependencies.

## Requirements
Python >= 3.8

## Installation

You can install `fastapy` from [PyPI](https://pypi.org/project/fastapy/):

```bash
pip install fastapy
```

or directly from GitHub:

```bash
pip install "git+https://github.com/aziele/fastapy.git"
```

You can also use `fastapy` without installation since it doesn't have any dependencies. Simply clone or download this repository and you're ready to use it.

```bash
git clone https://github.com/aziele/fastapy.git
cd fastapy
python
>>> import fastapy
>>> fastapy.__doc__
'A lightweight Python module to read and write FASTA sequence records'
```

## Quick Start
Typical usage is to read a FASTA file and loop over the sequences record(s).

```python
import fastapy

for record in fastapy.parse('tests/test.fasta'):
    print(record.id, len(record), record.seq[:10], record.desc)
```

Output:

```
NP_002433.1  362   METDAPQPGL   RNA-binding protein Musashi homolog 1 [Homo sapiens]
ENO94161.1    79   MKLLISGLGP   RRM domain-containing RNA-binding protein
sequence     292   MKLSKIALMM
```

## Usage
This module contains the `Record` class representing a FASTA sequence record and the `parse()` function to read FASTA records from a file.

### Record object
Record is an object that contains information on a FASTA sequence record, including id, description, and the sequence itself.

```python
import fastapy

record = fastapy.Record(
    id='NP_950171.2', 
    seq='MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFASICRKRQE',
    desc='APITD1-CORT protein isoform 2 [Homo sapiens]'
)

print(record.id)            # NP_950171.2
print(record.desc)          # APITD1-CORT protein isoform 2 [Homo sapiens]
print(record.seq)           # MEEEAE..
print(record.description)   # >NP_950171.2 G APITD1-CORT protein isoform 2 [Homo sapiens]
print(len(record))          # 77
print('EEEA' in record)     # True
```

By default, the sequence line is wrapped to 70 characters. You can provide the line length. Use zero (or None) for no wrapping.

```python
print(record)
# >NP_950171.2 APITD1-CORT protein isoform 2 [Homo sapiens]
# MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFAS
# ICRKRQE

print(record.format(wrap=30))
# >NP_001382951.1 G protein subunit gamma 5 [Homo sapiens]
# MEEEAETEEQQRFSYQQRLKAAVHYTVGCL
# CEEVALDKEMQFSKQTIAAISELTFRQCEN
# FAKDLEMFASICRKRQE

print(record.format(wrap=None))
# >NP_950171.2 APITD1-CORT protein isoform 2 [Homo sapiens]
# MEEEAETEEQQRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFASICRKRQE
```

### parse
The `parse()` function is a generator to read FASTA records as `Record` objects one by one from a file (plain FASTA or compressed using gzip or bzip2). Because only one record is created at a time, very little memory is required.

```python
import fastapy

for record in fastapy.parse('tests/test.fasta.gz'):
    print(record.id)
```

For some tasks you may need to have a reusable access to the records. For this purpose, you can use the built-in Python `list()` function to turn the iterator into a list:

```python
import fastapy

records = list(fastapy.parse('tests/test.fasta.gz'))
print(records[0].id)   # First record
print(records[-1].id)  # Last record
```

Another common task is to index your records by sequence identifier. Use `to_dict()` to turn a Record iterator (or list) into a dictionary.

```python
import fastapy

records = fastapy.to_dict(fasta.parse('tests/test.fasta.gz'))
print(records['NP_002433.1'])   # Use any record id
```

### read
The `read()` function reads only the first FASTA record from a file. It does not read any subsequent records in the file.

```python
import fastapy

seq_record = fastapy.read('tests/test.fasta')
print(seq_record.id)           # NP_002433.1
```

## Test
You can run tests to ensure that the module works as expected.

```
python -m unittest discover
```

## License

[GNU General Public License, version 3](https://www.gnu.org/licenses/gpl-3.0.html)

fastapy

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