just print sequence

[colindaven]

I'm writing a very simple demultiplexer (based on custom barcodes, first 8chars of the read) but am struggling to get the sequence out.

I've tried

seqrec.normalize
seqrec.seq

yet only get numbers, not sequence (here FASTQ, ATGCN expected) out.

    while let Some(record) = reader.next() {
        let seqrec = record.expect("invalid record");

        // demultiplex 

        // get sequence
        let sequence = seqrec.normalize(false);

        println!("Seq: {:?}", &sequence );

Results in

Seq: [71, 65, 84, 65, 84, 84, 67, 65, 65, 65, 84, 65, 65, 67, 67, 67, 84, 71, 65, 65, 65, 67, 65, 65, 65, 84, 71, 67, 84, 84, 65, 71, 71, 71, 65, 84, 84, 84, 84, 65, 84, 84, 71, 71, 84, 65, 84, 67, 65, 71, 71, 71, 84, 84, 65, 65, 84, 67, 71, 84, 71, 67, 67, 65, 65, 71, 65, 65, 65, 65, 71, 67, 71, 71, 67, 65, 84, 71, 71, 84, 67, 65, 65, 84, 65, 84, 65, 65, 67, 67, 65, 71]

The FASTQ looks ok

@NB551160:355:H2NG7BGXH:1:11101:3879:1050 1:N:0:0
AATGTNCTTTGTGGAAAGGACGAAACACCGCTGCAGAGAAAGTCAGCGNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNANNNNGN
+
AAAAA#E6EEEAEAAEEEAEEAEEEAEEEAEEEEEEEEEEEEEEEEEE###E#################################A####E#

What am I missing? Thanks

[Keats]

It returns a byte slice. Use https://doc.rust-lang.org/std/str/fn.from_utf8.html if you want to print the actual string.

[colindaven]

Excellent, thanks. For others:

    while let Some(record) = reader.next() {
        let seqrec = record.expect("invalid record");

        // demultiplex 

        // get sequence
        let sequenceBytes = seqrec.normalize(false);

        let sequenceText = str::from_utf8(&sequenceBytes).unwrap();
        println!("Seq: {} ", &sequenceText);
}