[EMBOSS] shufflseq output redirection for multiple shuffles

[Anandkumar Surendrarao]

Thank you, Malcolm. Those are nifty tricks I was not aware of...

And thank you, as well, Peter.

Cheers,
Anand

On Wed, Nov 28, 2018 at 1:35 PM Cook, Malcolm <MEC at stowers.org> wrote:

> And, if you have Gnu Parallel installed, use it to run the command 5 times
> (remove the --dry to actually run the commands)
>
> $ parallel --dry shuffleseq input.fasta output{}.fasta :::: <(seq 5)
> shuffleseq input.fasta output1.fasta
> shuffleseq input.fasta output2.fasta
> shuffleseq input.fasta output3.fasta
> shuffleseq input.fasta output4.fasta
> shuffleseq input.fasta output5.fasta
>
>
> or use  xargs (remove the 'echo' to run the command):
>
> $seq 5 | xargs -i echo shuffleseq input.fasta output{}.fasta
> shuffleseq input.fasta output1.fasta
> shuffleseq input.fasta output2.fasta
> shuffleseq input.fasta output3.fasta
> shuffleseq input.fasta output4.fasta
> shuffleseq input.fasta output5.fasta
>
>
>
>  > -----Original Message-----
>  > From: EMBOSS <emboss-bounces+mec=stowers.org at mailman.open-
>  > bio.org> On Behalf Of Peter Rice
>  > Sent: Wednesday, November 28, 2018 2:59 AM
>  > To: Anandkumar Surendrarao <aksrao at ucdavis.edu>;
>  > emboss at mailman.open-bio.org
>  > Subject: Re: [EMBOSS] shufflseq output redirection for multiple shuffles
>  >
>  > **CAUTION: Non-Stowers email**
>  >
>  >
>  > Hi Anand,
>  >
>  > You can run shuffleseq 5 times, with one shuffle (the default) and give
>  > a different output filename each time.
>  >
>  > shuffleseq input.fasta output1.fasta
>  >
>  > and so on...
>  >
>  > Hope that helps
>  >
>  > Peter Rice
>  > EMBOSS Team
>  >
>  > On 28/11/2018 03:57, Anandkumar Surendrarao wrote:
>  > > Greetings!
>  > >
>  > > If I have a multifasta file - lets say input.fasta with 5 chromosomal
>  > > sequences,
>  > > and I want to shuffle the entire genome 5 times,
>  > >
>  > > how can I redirect each of the 5 shuffled genomes to a
>  > > different filename - output1.fasta, ... output5.fasta?
>  > >
>  > > Currently, my syntax redirects all 5 shuffled versions to the same
>  > > output filename, which is not optimal. Any suggestions?
>  > >
>  > > Thanks a bunch.
>  > >
>  > > - Anand
>  > > _____
>  > > *Anandk*umar *S*urendra*rao*, PhD
>  > > +1.530.574.5134
>  > > +91.91760.70887
>  > >
>  > >
>  > >
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