https://github.com/mdshw5/strandex
Sample an approximate number of reads from a fastq file without reading the entire file
https://github.com/mdshw5/strandex
bioinformatics fastq regex
Last synced: 5 months ago
JSON representation
Sample an approximate number of reads from a fastq file without reading the entire file
- Host: GitHub
- URL: https://github.com/mdshw5/strandex
- Owner: mdshw5
- License: mit
- Created: 2015-05-15T23:54:47.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2017-06-20T00:40:22.000Z (over 8 years ago)
- Last Synced: 2024-03-25T14:46:21.625Z (over 1 year ago)
- Topics: bioinformatics, fastq, regex
- Language: Python
- Size: 22.5 KB
- Stars: 11
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# strandex
**strand**-anchored reg**ex** for uniform sampling from FASTQ files (think **spandex**)
[](https://travis-ci.org/mdshw5/strandex)
[](https://pypi.python.org/pypi/strandex)
[](https://landscape.io/github/mdshw5/strandex/master)
[](https://codecov.io/gh/mdshw5/strandex)
## Why use this?
- You want only a few reads from a large FASTQ file (**downsampling**)
- You are constrained by I/O so that reading through the entire file is very slow
- You want to avoid sampling only the beginning or end of the file
- You want to expand a small FASTQ file to a specific number of reads (**upsampling**)
## Caveats
- For paired-end sampling, reads in both files must be in the same order and have the same length
- For sampling `n` reads approximately equal to the total available, sampling with replacement may occur
# Install
`pip install strandex`
# Examples
```
from strandex import FastqSampler
sampler = FastqSampler('read1.fastq', fastq2='read2.fastq', nreads=100000, seed=42)
for read1, read2 in sampler:
# read1 and read2 are 4-line strings sampled from paired input
sampler = FastqSampler('read1.fastq', nreads=100000, seed=42)
for read1, read2 in sampler:
# read1 is a 4-line string sampled from input
# read2 is NoneType
```
Note that you may sample more reads *than are available in your input file*. In
the event that you want to sample more reads than your input file contains, strandex
will sample the file with replacement, meaning you will get some duplicate reads.
# CLI script
```
usage: strandex [-h] [-fq2 FASTQ2] [-o2 OUT2] [-n NREADS] [-s SEED] fastq1 out
sample uniformly without reading an entire fastq file
positional arguments:
fastq1 input fastq file
out output fastq file
optional arguments:
-h, --help show this help message and exit
-fq2 FASTQ2, --fastq2 FASTQ2
input fastq file read pairs
-o2 OUT2, --out2 OUT2
output fastq file read pairs
-n NREADS, --nreads NREADS
number of reads to sample from input (default: 1)
-s SEED, --seed SEED seed for random number generator (default: None)
-t TRIM, --trim TRIM trim reads to length -t (default: None)
```