| Name | fastQpick JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | None |
| Summary | Fast and memory-efficient sampling of DNA-Seq or RNA-seq fastq data with or without replacement. |
| upload_time | 2025-01-22 23:02:48 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | BSD 2-Clause License
Copyright (c) 2024, Pachter Lab
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
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2. Redistributions in binary form must reproduce the above copyright notice,
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
| keywords |
fastqpick
bioinformatics
statistics
rna-seq
dna-seq
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
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# fastQpick
Fast and memory-efficient sampling of DNA-seq or RNA-seq FASTQ data with or without replacement.
---
## Installation
### Install via PyPI
```bash
pip install fastQpick
```
### Install from Source Code
Using pip:
```bash
pip install git+https://github.com/pachterlab/fastQpick.git
```
Or clone the repository and build manually:
```bash
git clone https://github.com/pachterlab/fastQpick.git
cd fastQpick
python -m build
python -m pip install dist/fastQpick-x.x.x-py3-none-any.whl
```
---
## Usage
### Command-line Interface
Run `fastQpick` with a specified fraction and options:
```bash
fastQpick --fraction FRACTION [OPTIONS] FASTQ_FILE1 FASTQ_FILE2 ...
```
### Python API
Use `fastQpick` in your Python code:
```python
from fastQpick import fastQpick
fastQpick(
input_file_list=['FASTQ_FILE1', 'FASTQ_FILE2', ...],
fraction=FRACTION,
...
)
```
---
## Documentation
- **Command-line Help**: Use the following command to see all available options:
```bash
fastQpick --help
```
- **Python API Help**: Use the `help` function to explore the API:
```python
help(fastQpick)
```
### Options
- input_files (str, list, or tuple) List of input FASTQ files or directories containing FASTQ files. Required. Positional argument on command line.
- fraction (int or float) The fraction of reads to sample, as a float greater than 0. Any value equal to or greater than 1 will turn on the -r flag automatically.
- seed (int or str) Random seed(s). Can provide multiple seeds separated by commas. Default: 42
- output_dir (str) Output directory. Default: ./fastQpick_output
- gzip_output (bool) Whether or not to gzip the output. Default: False (uncompressed)
- group_size (int) The size of grouped files. Provide each pair of files sequentially, separated by a space. E.g., I1, R1, R2 - would have group_size=3. Default: 1 (unpaired)
- replacement (bool) Sample with replacement. Default: False (without replacement).
- overwrite (bool) Overwrite existing output files. Default: False
- low_memory (bool) Whether to use low memory mode (uses ~5.5x less memory than default, but adds marginal time to the data - structure generation preprocessing). Default: False
- verbose (bool) Whether to print progress information. Default: True
---
## Features
- Efficient sampling of large FASTQ files.
- Works with both single and paired-end sequencing data.
- Supports sampling with or without replacement.
- Command-line interface and Python API for seamless integration.
- Memory efficient - in low-memory mode, only uses as much memory as a list of (small) integers the length of the number of reads in the fastq file for each file.
- Time efficient - only passes through the fastq once and writes to output in batches - can process 600M reads in 10-15 minutes
## Low memory mode vs. standard
Low memory mode vs. standard, when fraction=1 (i.e., number of reads to sample is the same as the number of reads in the fastq):
- Adds an extra ~1-3 seconds per million reads per group_size (i.e., 500M reads would take 30 minutes instead of 20-25 minutes)
- Saves an extra ~40MB RAM per million reads (i.e., 500M reads would take 3.75GB RAM vs 20.6GB RAM)
---
## Examples
### 1. Sample 10% of reads with replacement from a FASTQ file:
**Command-line**
```bash
fastQpick --fraction 0.1 -r input.fastq
```
**Python**
```python
from fastQpick import fastQpick
fastQpick(
input_files='input.fastq',
fraction=0.1,
replacement=True
)
```
### 2. Sample 100% of reads with replacement from multiple paired FASTQ files (R1, R2) across three seeds (i.e., bootstrapping):
**Command-line**
```bash
fastQpick --fraction 1 -s 42,43,44 -r -g 2 input1_R1.fastq input1_R2.fastq
```
**Python**
```python
from fastQpick import fastQpick
fastQpick(
input_files='input.fastq',
fraction=1,
seed="42,43,44",
replacement=True,
group_size=2,
)
```
---
## License
fastQpick is licensed under the 2-clause BSD license. See the [LICENSE](LICENSE) file for details.
---
## Contributing
We welcome contributions! Please see the [CONTRIBUTING.md](CONTRIBUTING.md) file for guidelines on how to get involved.
Raw data
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"description": "# fastQpick\n\nFast and memory-efficient sampling of DNA-seq or RNA-seq FASTQ data with or without replacement.\n\n---\n\n## Installation\n\n### Install via PyPI\n```bash\npip install fastQpick\n```\n\n### Install from Source Code\n\nUsing pip:\n```bash\npip install git+https://github.com/pachterlab/fastQpick.git\n```\n\nOr clone the repository and build manually:\n```bash\ngit clone https://github.com/pachterlab/fastQpick.git\ncd fastQpick\npython -m build\npython -m pip install dist/fastQpick-x.x.x-py3-none-any.whl\n```\n\n---\n\n## Usage\n\n### Command-line Interface\n\nRun `fastQpick` with a specified fraction and options:\n```bash\nfastQpick --fraction FRACTION [OPTIONS] FASTQ_FILE1 FASTQ_FILE2 ...\n```\n\n### Python API\n\nUse `fastQpick` in your Python code:\n```python\nfrom fastQpick import fastQpick\n\nfastQpick(\n input_file_list=['FASTQ_FILE1', 'FASTQ_FILE2', ...],\n fraction=FRACTION,\n ...\n)\n```\n\n---\n\n## Documentation\n\n- **Command-line Help**: Use the following command to see all available options:\n ```bash\n fastQpick --help\n ```\n\n- **Python API Help**: Use the `help` function to explore the API:\n ```python\n help(fastQpick)\n ```\n\n### Options\n- input_files (str, list, or tuple) List of input FASTQ files or directories containing FASTQ files. Required. Positional argument on command line.\n- fraction (int or float) The fraction of reads to sample, as a float greater than 0. Any value equal to or greater than 1 will turn on the -r flag automatically.\n- seed (int or str) Random seed(s). Can provide multiple seeds separated by commas. Default: 42\n- output_dir (str) Output directory. Default: ./fastQpick_output\n- gzip_output (bool) Whether or not to gzip the output. Default: False (uncompressed)\n- group_size (int) The size of grouped files. Provide each pair of files sequentially, separated by a space. E.g., I1, R1, R2 - would have group_size=3. Default: 1 (unpaired)\n- replacement (bool) Sample with replacement. Default: False (without replacement).\n- overwrite (bool) Overwrite existing output files. Default: False\n- low_memory (bool) Whether to use low memory mode (uses ~5.5x less memory than default, but adds marginal time to the data - structure generation preprocessing). Default: False\n- verbose (bool) Whether to print progress information. Default: True\n\n---\n\n## Features\n\n- Efficient sampling of large FASTQ files.\n- Works with both single and paired-end sequencing data.\n- Supports sampling with or without replacement.\n- Command-line interface and Python API for seamless integration.\n- Memory efficient - in low-memory mode, only uses as much memory as a list of (small) integers the length of the number of reads in the fastq file for each file.\n- Time efficient - only passes through the fastq once and writes to output in batches - can process 600M reads in 10-15 minutes\n\n## Low memory mode vs. standard\nLow memory mode vs. standard, when fraction=1 (i.e., number of reads to sample is the same as the number of reads in the fastq):\n- Adds an extra ~1-3 seconds per million reads per group_size (i.e., 500M reads would take 30 minutes instead of 20-25 minutes)\n- Saves an extra ~40MB RAM per million reads (i.e., 500M reads would take 3.75GB RAM vs 20.6GB RAM)\n\n---\n\n## Examples\n\n### 1. Sample 10% of reads with replacement from a FASTQ file:\n\n**Command-line**\n```bash\nfastQpick --fraction 0.1 -r input.fastq\n```\n\n**Python**\n```python\nfrom fastQpick import fastQpick\n\nfastQpick(\n input_files='input.fastq',\n fraction=0.1,\n replacement=True\n)\n```\n\n### 2. Sample 100% of reads with replacement from multiple paired FASTQ files (R1, R2) across three seeds (i.e., bootstrapping):\n\n**Command-line**\n```bash\nfastQpick --fraction 1 -s 42,43,44 -r -g 2 input1_R1.fastq input1_R2.fastq\n```\n\n**Python**\n```python\nfrom fastQpick import fastQpick\n\nfastQpick(\n input_files='input.fastq',\n fraction=1,\n seed=\"42,43,44\",\n replacement=True,\n group_size=2,\n)\n```\n---\n\n## License\n\nfastQpick is licensed under the 2-clause BSD license. See the [LICENSE](LICENSE) file for details.\n\n---\n\n## Contributing\n\nWe welcome contributions! Please see the [CONTRIBUTING.md](CONTRIBUTING.md) file for guidelines on how to get involved.\n\n",
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