Crate fasten_regex

Filter reads based on a regular expression.

Examples

Find a specific read

cat file.fastq | fasten_regex --which ID --regex 'my-specific-read-id-1234' > my_read.fastq

Find a specific read but also keep its pair

cat file.fastq | fasten_regex --which ID --regex 'my-specific-read-id-1234' --paired-end > my_pairs.fastq

Find a specific motif

cat file.fastq | fasten_regex --which SEQ --regex ATAT > atat-motif.fastq

Usage

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

Functions

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