[mira_talk] Re: MIRA 4.0.1 mirabait -f fromtype problem
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 12 May 2014 09:38:39 +0100
Hi Bastien,
Is this the mirabait bug you mentioned fixing in MIRA 4.0.2?
//www.freelists.org/post/mira_talk/MIRA-401-released,3
Thanks,
Peter
On Mon, Apr 14, 2014 at 4:03 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
> Hi Bastien,
>
> When using MIRA in combination with Galaxy, all the datafiles
> typically end with the extension *.dat so I have been explicitly
> telling MIRA the file types via command line options etc.
>
> This used to work on MIRA 4.0 but now fails on MIRA 4.0.1,
>
> $ /mnt/galaxy/downloads/mira_4.0.1_linux-gnu_x86_64_static/bin/mirabait
> -f fastq -t fastq -k 32 -n 50 bait.dat input.dat output_stem
> input.dat 1 2 input 3 dat
> mirabait (MIRALIB version 4.0.1)
> Author: Bastien Chevreux (bach@xxxxxxxxxxxx)
>
> ... baiting ...
> Usage:
> mirabait [-f <fromtype>] [-t <totype> [-t <totype> ...]] [-ikLor]
> baitfile infile <basename_for_outfile(s)>
>
> Options:
> -f <fromtype> load this type of project files, where fromtype is:
> caf sequences from CAF
> maf sequences from MAF
> phd sequences from a PHD
> gbf sequences from a GBF
> fasta sequences from a FASTA
> fastq sequences from a FASTQ
> -t <totype> write the sequences to this type (multiple mentions
> of -t are allowed):
> fasta sequences to FASTA
> fastq sequences to FASTQ
> caf sequences to CAF
> maf sequences to MAF
> txt sequence names to text file
>
> -L Do not compute hash statistics, load from baitfile
> (which the must be a mirabait hash statistics file).
>
> -k k-mer, length of bait in bases (<32, default=31)
> -n Min. number of k-mer baits needed (default=1)
> -i Inverse hit: writes only sequences that do not hit bait
> -r No checking of reverse complement direction
>
> -o fastq quality Offset (only for -f = 'fastq')
> Offset of quality values in FASTQ file. Default: 33
> A value of 0 tries to automatically recognise.
>
> Examples:
> ...
> ...
>
> Unknown or illegal file type 'dat' defined as <fromtype>
>
>
>
> Hopefully that is enough to reproduce the error,
>
> Thanks,
>
> Peter
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