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 <[email protected]
> bio.org> On Behalf Of Peter Rice
> Sent: Wednesday, November 28, 2018 2:59 AM
> To: Anandkumar Surendrarao <[email protected]>;
> [email protected]
> 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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> > [email protected]
> > http://mailman.open-bio.org/mailman/listinfo/emboss
> >
>
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