SEQIO fetching the record Id

Question

[GR]

Hi All,

I am using SEQIO to parse a fastq file. When I fetch the record.id then it does not fetch the full id like

my id: @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG

seqio record.id: @EAS139:136:FC706VJ:2:2104:15343:197393

I am wondering why it is not considering the full id, i.e, the characters after space. I can easily fix this by using sed (replacing space with some other char) but I am wondering if I can fix this with SEQIO.

Thanks.

[Peter]

The identifier in FASTQ (and FASTA) is the first word, here EAS139:136:FC706VJ:2:2104:15343:197393 while the rest is considered a comment, 1:Y:18:ATCACG

P.S. I presume the @ here was just the new record marker in your FASTQ file - that is not part of the ID either.

[GR]

Thanks Peter. You are right indeed, '@' was a typo from my side.

Answer 1

[Devon Ryan]

It is getting the full ID, the "1:Y:18:ATCACG" portion isn't part of the ID. You can get this in record.description if you really want it.