seqkit won't wrap to 60 nt per line

[plijnzaad]

I'm trying to convert a nanopore fastq file to a fasta file using 60 nucleotides per line, but am failing, with all of :

zcat PBM11090_pass_f7cf4b5f_8bda2ae4_11-GT100k.fastq.gz  | seqkit fq2fa  > foo.fa

zcat PBM11090_pass_f7cf4b5f_8bda2ae4_11-GT100k.fastq.gz  | seqkit fq2fa  -w 60 -o foo.fa.gz

zcat PBM11090_pass_f7cf4b5f_8bda2ae4_11-GT100k.fastq.gz  | seqkit convert -w 60  -o foo.fa.gz

I'm just getting the original, unwrapped sequence.

The reason I'm using the zcat ... | construct above is that using -f file does not work; see issue #102 and my comment

BTW, this concerns a fastq file with exactly one sequence that is longer than 100k nt's.

[shenwei356]

All commands output FASTQ without wrapping the sequence lines :( Back to several years ago, most data were short reads, and people did not want 100-150bp short reads to be wrapped by default.

This should be changed now. I'll allow wrapping fastq when users explicitly specify -w, --line-width.

[shenwei356]

Wait, I found fq2fa does not wrap the fasta format ~ Currently, you can pipe the result to other commands like seqkit seq.

zcat PBM11090_pass_f7cf4b5f_8bda2ae4_11-GT100k.fastq.gz  | seqkit fq2fa | seqkit seq -w 60 > foo.fa

[shenwei356]

Fixed fq2fa and made other commands wrap sequences and qualities when explicitly specifying the line width (-w).

• seqkit_windows_amd64.exe.tar.gz
• seqkit_linux_amd64.tar.gz
• seqkit_darwin_arm64.tar.gz