Crate fasten_replace

Streaming editor for fastq data using a find/replace.

Examples

Force a motif to be lowercase

cat file.fastq | fasten_replace --which SEQ --find ATAT --replace atat > file.fastq

Mutate the middle base of a kmer

cat file.fastq | fasten_replace --which SEQ --find AAAAA --replace AATAA > file.fastq

# Usage
 
Usage: fasten_replace [-h] [-n INT] [-p] [-v] [-f STRING] [-r STRING] [-w STRING]
 
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
    -f, --find STRING   Regular expression (default: '.')
    -r, --replace STRING
                        String to replace each match
    -w, --which STRING  Which field to match on? ID, SEQ, QUAL. Default: SEQ

Functions

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