| Name | pyfastatools JSON |
| Version |
2.5.0
JSON |
| download |
| home_page | None |
| Summary | Simple FASTA file tools to parse, edit, subset, split, and perform stats on FASTA files |
| upload_time | 2025-02-07 23:08:21 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | MIT License
Copyright (c) 2023 Cody Martin
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
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# FASTA file parsing written in C++ with Python bindings
## Installation
```bash
pip install pyfastatools
```
## Usage
The `pyfastatools.Parser` object is the primary API that parses FASTA files and yields `pyfastatools.Record` objects.
If you have a FASTA file called `proteins.faa` that looks like this:
```txt
>seq_1
MSKFKKIPL
>seq_2
MQSSSKTCN
>seq_3
MEDNMITIY
```
Then you can parse this file in python like this:
```python
from pyfastatools import Parser
for record in Parser("proteins.faa"):
print(record.header.name, record.seq)
```
which will print:
```python
>>> 'seq_1 MSKFKKIPL'
>>> 'seq_2 MQSSSKTCN'
>>> 'seq_3 MEDNMITIY'
```
## API
This library has a very simple API that can be displayed in a few lines:
### Parser
This is the main class that will satisfy 99% of user needs. While parsing FASTA files, it produces `Record` objects. Only the name of a FASTA file is needed:
```python
pyfastatools.Parser("my_fasta.fasta")
```
The parser will attempt to auto-detect the `RecordType` of the file by checking the input file extension and the first 5 sequences.
However, the record type can optionally be specified:
```python
pyfastatools.Parser("my_fasta.fasta", pyfastatools.RecordType.PROTEIN)
```
The parser can be iterated over to yield one `Record` at a time:
```python
parser = pyfastatools.Parser("my_fasta.fasta")
for record in parser:
...
```
#### Methods
There are also other convenience methods:
- `all` - Read all records into a list-like object.
- `take` - Take up to n records into a list-like object.
- `filter` - Keep/exclude sequences based on the sequence name.
- `remove_stops` - Yield sequences without a `*` stop codon character if the sequences are proteins.
- `clean_header` - Yield sequences while cleaning the header to not have a description.
- `headers` - Yield `Header` objects only without parsing the sequence itself.
- `all_headers` - Return all headers into a list-like object.
#### Properties
- `num_records` - Returns the number of sequences in the FASTA file. This is cached after the first time it is called. Note: This can also be computed using `len(parser)`
- `format` - Returns the `RecordType` enum that corresponds to the FASTA file's record type
- `extension` - Returns the file extension based on the `format`
### Record
A single FASTA record. It has the following fields:
- `header` - A `Header` object that has the fields `name` and `desc`
- `seq` - A `str` storing the entire sequence
#### Methods
- `empty` - Checks if the `Header` and sequence are empty
- `clear` - Sets the `Header` and sequence to empty strings
- `to_string` - Returns the record as a string representation identical to what was parsed from the file
- `clean_header` - Sets the `Header` description to an empty string
- `remove_stops` - Removes `*` stop codon characters from the sequence if they are present
Raw data
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"description": "# FASTA file parsing written in C++ with Python bindings\n\n## Installation\n\n```bash\npip install pyfastatools\n```\n\n## Usage\n\nThe `pyfastatools.Parser` object is the primary API that parses FASTA files and yields `pyfastatools.Record` objects.\n\nIf you have a FASTA file called `proteins.faa` that looks like this:\n\n```txt\n>seq_1\nMSKFKKIPL\n>seq_2\nMQSSSKTCN\n>seq_3\nMEDNMITIY\n```\n\nThen you can parse this file in python like this:\n\n```python\nfrom pyfastatools import Parser\n\nfor record in Parser(\"proteins.faa\"):\n print(record.header.name, record.seq)\n```\n\nwhich will print:\n\n```python\n>>> 'seq_1 MSKFKKIPL'\n>>> 'seq_2 MQSSSKTCN'\n>>> 'seq_3 MEDNMITIY'\n```\n\n## API\n\nThis library has a very simple API that can be displayed in a few lines:\n\n### Parser\n\nThis is the main class that will satisfy 99% of user needs. While parsing FASTA files, it produces `Record` objects. Only the name of a FASTA file is needed:\n\n```python\npyfastatools.Parser(\"my_fasta.fasta\")\n```\n\nThe parser will attempt to auto-detect the `RecordType` of the file by checking the input file extension and the first 5 sequences.\n\nHowever, the record type can optionally be specified:\n\n```python\npyfastatools.Parser(\"my_fasta.fasta\", pyfastatools.RecordType.PROTEIN)\n```\n\nThe parser can be iterated over to yield one `Record` at a time:\n\n```python\nparser = pyfastatools.Parser(\"my_fasta.fasta\")\nfor record in parser:\n ...\n```\n\n#### Methods\n\nThere are also other convenience methods:\n\n- `all` - Read all records into a list-like object.\n- `take` - Take up to n records into a list-like object.\n- `filter` - Keep/exclude sequences based on the sequence name.\n- `remove_stops` - Yield sequences without a `*` stop codon character if the sequences are proteins.\n- `clean_header` - Yield sequences while cleaning the header to not have a description.\n- `headers` - Yield `Header` objects only without parsing the sequence itself.\n- `all_headers` - Return all headers into a list-like object.\n\n#### Properties\n\n- `num_records` - Returns the number of sequences in the FASTA file. This is cached after the first time it is called. Note: This can also be computed using `len(parser)`\n- `format` - Returns the `RecordType` enum that corresponds to the FASTA file's record type\n- `extension` - Returns the file extension based on the `format`\n\n### Record\n\nA single FASTA record. It has the following fields:\n\n- `header` - A `Header` object that has the fields `name` and `desc`\n- `seq` - A `str` storing the entire sequence\n\n#### Methods\n\n- `empty` - Checks if the `Header` and sequence are empty\n- `clear` - Sets the `Header` and sequence to empty strings\n- `to_string` - Returns the record as a string representation identical to what was parsed from the file\n- `clean_header` - Sets the `Header` description to an empty string\n- `remove_stops` - Removes `*` stop codon characters from the sequence if they are present\n",
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"license": "MIT License\n \n Copyright (c) 2023 Cody Martin\n \n Permission is hereby granted, free of charge, to any person obtaining a copy\n of this software and associated documentation files (the \"Software\"), to deal\n in the Software without restriction, including without limitation the rights\n to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n copies of the Software, and to permit persons to whom the Software is\n furnished to do so, subject to the following conditions:\n \n The above copyright notice and this permission notice shall be included in all\n copies or substantial portions of the Software.\n \n THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n SOFTWARE.",
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