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Batch fastq_to_fasta: how to append output file name? #107

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Opinel99 opened this issue Mar 2, 2018 · 1 comment
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Batch fastq_to_fasta: how to append output file name? #107

Opinel99 opened this issue Mar 2, 2018 · 1 comment

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@Opinel99
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Opinel99 commented Mar 2, 2018

This is all quite new to me so I apologize in advance:

I would like to have a script that will do a batch fastq_to_fasta conversion with seperate output files with appended names, e.g.:
X.fastq > X.fasta
Y.fastq > Y.fasta
Z.fastq > Z.fasta

There must be an easy way to do this but I just can't figure out the output...

@lh3
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lh3 commented Mar 5, 2018

ls *.fastq | sed s,q$,, | xargs -i echo seqtk seq -a {}q > {}a | sh

If you have GNU parallel installed:

ls *.fastq | sed s,q$,, | xargs -i echo seqtk seq -a {}q > {}a | parallel

@lh3 lh3 closed this as completed Mar 5, 2018
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