[mira_talk] Re: Request for Comments: mirabait for paired-end
- From: Martin MOKREJŠ <mmokrejs@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 24 Jun 2014 15:52:14 +0200
Bastien Chevreux wrote:
Hi Bastien,
> Dear all,
>
> for different reasons, implementing a mirabait version aware of paired-end
> was not quite straightforward with the code-base of MIRA 4.0.x. However, as
> the need for it also arose also for my daily work, I have implemented the
> necessary changes in the past weeks.
>
> I am foreseeing some changes in the default behaviour of mirabait as well as
> for the command line. This would probably break scripts using mirabit with
> the “old” syntax and I would like some feedback of what people think. Nothing
> is implemented yet, so there’s a couple of days to think things through.
>
> Currently, the default behaviour of mirabait is this: it is not aware of
> paired-ends; it reads a file containing bait sequences, reads one or several
> files with sequences to search and writes to one(!) output file all sequences
> which either a) match on the kmer level the bait sequence or(!) b) the
> sequences which do NOT match (the -i option of mirabait). The command line
> looks like this atm:
>
> mirabait [options] {bait_file} {input_file} [[input_file_2 input_file_3
> ...]] {output_basename}
I propose renaming mirabait to say mirabait2 to emphasize the different syntax.
Just do not stick to the current name, please.
> I have a couple of questions:
>
> 1) atm I plan to disallow writing results in multiple formats at the same
> time. E.g., one could not have results written both as FASTQ and FASTA at the
> same time (which is possible with the current mirabait). Any problem with
> that?
No, there are tools to convert FASTQ to FASTA.
> 2) would it make sense to allow mirabait read bait sequences from multiple
> files? If yes, would it make sense to change the command line so that each
> bait file (even if only one is wanted) needs an option like, e.g.
> mirabait … -b baitfile1 -b baitfile2 …
> As added bonus of a forced ‘-b’: mirabait would stop on old syntax (which
> did not have -b) and tell the user to adapt his command.
>
> 3) I am planning to set up mirabait to act as a file splitter instead of a
> file filter. I.e., instead of filtering and writing to an output file only
> sequences (not) matching the bait sequences, the new version could sort the
> sequences matching to one output file and sequences not matching to another
> output file. Default would be to have only the matching output active, but a
> switch would allow to either also add the non matching or to write only the
> non-matching.
I would prefer options like -i (include) and -e (exclude) and -p (prefix).
>
> 4) Would it make sense to have mirabait write results for each input file
> into a separate output file as default? That would enable other tools
> (assembler, mappers, whatever) to directly work with Illumina paired-end
> which is almost always in two files. The downside: when writing to separate
> files, I think it is almost impossible to have the user name every
> outputfile. So the default behaviour would be to name the output files like
> the input files, but with a given prefix. E.g. “baithits_” for sequences
> which matched and “baitmiss_” for sequences which did not.
No idea.
Martin
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