[EMBOSS] shufflseq output redirection for multiple shuffles

[Cook, Malcolm]

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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 > > EMBOSS mailing list
 > > EMBOSS at mailman.open-bio.org
 > > http://mailman.open-bio.org/mailman/listinfo/emboss
 > >
 > 
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