strand-anchored regex for uniform sampling from FASTQ files (think spandex)
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)
- For paired-end sampling, reads in both files must be in the same order and have the same length
- For sampling
nreads approximately equal to the total available, sampling with replacement may occur
pip install strandex
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.
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)