orient-seqs: accept FASTQ data as input

[nbokulich]

vsearch --orient can accept FASTQ as input (and also output via the --fastqout 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.

[colinvwood]

Links to motivating forum posts here and here for reference.

[mirand863]

Hi,

Thank you very much for opening this issue! I made some progress today. It is working with a single end FASTQ file using the type MultiplexedSingleEndBarcodeInSequence and I believe it would not be too much trouble to allow for other types, i.e., paired end and multiple samples inside a folder. However, I am currently running into an error is not complete type expression with the TypeMap. I will try to debug more another day to solve this error.

Best regards,
Fabio