strandex 0.3.1

Strand-anchored regex for expansion or contraction of FASTQ files

# 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://coveralls.io/r/mdshw5/strandex?branch=master)

##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**)

# 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)
```