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fastapy-1.0.3
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مشاهده بیشترتوضیحات
A lightweight Python module to read and write FASTA sequence records
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | fastapy-1.0.3 |
| نام | fastapy |
| نسخه کتابخانه | 1.0.3 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | Andrzej Zielezinski <a.zielezinski@gmail.com>, Maciej Michalczyk <mccv99@gmail.com> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/fastapy/ |
| مجوز | - |
# 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('test/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('test/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('test/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('test/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('test/test.fasta')
print(seq_record.id) # NP_002433.1
```
## Test
You can run tests to ensure that the module works as expected.
```
./test/test.py
```
## License
[GNU General Public License, version 3](https://www.gnu.org/licenses/gpl-3.0.html)
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl fastapy-1.0.3:
pip install fastapy-1.0.3.whl
نصب پکیج tar.gz fastapy-1.0.3:
pip install fastapy-1.0.3.tar.gz