1. Nicola Segata
  2. MetaPhlAn
  3. Issues
Issue #1 resolved

Please add option --O FileName to route output

Anonymous created an issue

Please create option "--O FileName" to route output to FileName

Thanks!

Comments (2)

  1. Nicola Segata repo owner

    Thanks for the suggestion. The output file could already be specified as a positional argument (in addition to standard output), but for better integration with other pipelines I also added now a non positional argument (-o or --output_file).

    So there are three options for specifying the output now.

    The standard output (redirected in this case to the file):

    ./metaphlan.py LC1.fna --bowtie2db bowtie2db/mpa > output_file.txt
    

    the positional argument

    ./metaphlan.py LC1.fna output_file.txt --bowtie2db bowtie2db/mpa
    

    and the new non-positional argument (-o, but also --output_file also works)

    ./metaphlan.py /tmp/LC1.fna --bowtie2db bowtie2db/mpa -o output_file.txt
    

    Thanks again for the suggestion. Nicola

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