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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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antropos detect output as fasta #20

Closed antonkulaga closed 7 years ago

antonkulaga commented 7 years ago

Current antropos detect output is some text file that I have to parse to make use of detected adapters. It will be very useful to be able to have an option to output as fasta instead, so I will be able to use it in the other steps of the pipeline.

jdidion commented 7 years ago

Great idea. I'll enable fasta and json output. Probably on Monday.

On May 20, 2017, at 8:02 PM, Anton Kulaga notifications@github.com wrote:

Current antropos detect output is some text file that I have to parse to make use of detected adapters. It will be very useful to be able to have an option to output as fasta instead, so I will be able to use it in the other steps of the pipeline.

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jdidion commented 7 years ago

Use a .fasta extension on the filename, or use --output-formats fasta. You can also use the --fasta option to specify whether fasta output should be a single file, one file per input, or both. This will be in the next release.