Crate fasten_shuffle

Interleaves reads from either stdin or file parameters.

Many fasten executables are aware of paired end reads but they need to be in interleaved format. This script transforms R1 and R2 reads into interleaved format.

Examples

Shuffling

Simple transformation of R1 and R2 into interleaved

cat file_1.fastq file_2.fastq | fasten_shuffle > interleaved.fastq
fasten_shuffle -1 file_1.fastq -2 file_2.fastq > interleaved.fastq

interleave R1 and R2 and pipe it into another executable with –paired-end

cat file_1.fastq file_2.fastq | fasten_randomize --paired-end | head -n 8 > random-pair.fastq

… or to another executable with –paired-end

cat file_1.fastq file_2.fastq | fasten_sample --paired-end --frequency 0.2 > downsample.20percent.fastq

Deshuffling

cat interleaved.fastq | fasten_shuffle -d -1 1.fastq -2 2.fastq

Usage

Usage: fasten_shuffle [-h] [-n INT] [-p] [-v] [-d] [-1 1.fastq] [-2 2.fastq]
 
Options:
    -h, --help          Print this help menu.
    -n, --numcpus INT   Number of CPUs (default: 1)
    -p, --paired-end    The input reads are interleaved paired-end
    -v, --verbose       Print more status messages
    -d, --deshuffle     Deshuffle reads from stdin
    -1 1.fastq          Forward reads. If deshuffling, reads are written to
                        this file.
    -2 2.fastq          Forward reads. If deshuffling, reads are written to
                        this file.

Functions

deshuffle

Read from stdin and deshuffle reads into files

main

read_seqs

Read fastq entries from a filename

shuffle

Read fastq from stdin and interleave