RESCRIPt: accepting FASTQ as input to `orient-seqs`

mirand863 · July 10, 2023, 5:46pm

Hi,

I could not find an issue on GitHub about using FASTQ in RESCRIPt's orient-seqs. I would like to know a bit more about the requirements and can work on it shortly.

Best regards,
Fabio

colinvwood · July 13, 2023, 5:11pm

Hello @mirand863,

That's awesome that you want to contribute! If there isn't an issue feel free to open one. It looks like the changes will involve updating the wrapper to vsearch --orient to accept and output qiime FASTQ types/formats and use a --fastqout option. In case you weren't aware the place to hop in will be here.

Nicholas_Bokulich · July 13, 2023, 6:43pm

Thanks @mirand863 and @colinvwood ! I have opened up an issue here so we can move discussion over there:

github.com/bokulich-lab/RESCRIPt

orient-seqs: accept FASTQ data as input

opened 06:42PM - 13 Jul 23 UTC

nbokulich

`vsearch --orient` can accept FASTQ as input (and also output via the `--fastqou…t` option). Ideally, `orient-seqs` (which is just thinly wrapping `vsearch --orient`) could do the same. This would require modifying the inputs/outputs here: https://github.com/bokulich-lab/RESCRIPt/blob/master/rescript/orient.py#L55 HOWEVER, the main issue I see is that the current inputs and outputs are `DNAFASTAFormat` objects. A FASTQ-formatted input (e.g., coming from some of the `SampleData[.*Sequence.*]` types) could not have `DNAFASTAFormat` as a view type. I suppose we need something like a `Union[SingleLanePerSamplePairedEndFastqDirFmt | DNAFASTAFormat | ... ]` as input and output, and a `TypeMap` in the plugin registration to accept and output the corresponding types.

(also splitting this discussion off to a separate topic in #dev-discussion )