bioawk output in original fastq format

Question

[weixiaokuan]

Hi, I was trying to use bioawk to extract some matched sequences from a fastq file. However, the output is somehow tabular format of fastx with $name, $seq, $qual and $comment. Did anyone know if there is an option from bioawk which can make the output keep the original fastq 4 line format? I know I can use script to process the output to make it similar as original fastq format, but if bioawk has an option for such type output, it will be very nice. Thank you.

Xiaokuan

[cpad0112]

refer to post on searching fastq files: searching reads with a certain sequence in fastq file

Answer 1

[Stephane Plaisance]

bioawk -c fastx '{print "@"$name" "$comment"\n"$seq"\n+\n"$qual}' input.fq > output.fq

this should output a duplcate of the input, add more code to filter or modify any