• jhoogenboom's avatar
    Reworked input/output file arguments · 7f23c2e0
    jhoogenboom authored
    * All tools now write to stdout by default. Tools that support
      writing report files write those to stderr by default. The
      -o/--output and -r/--report options can be used to override
    * Tools that operated on one sample at a time (bgcorrect,
      seqconvert, stuttermark) now support batch processing. The new
      -i/--input argument takes a list of files. In batch mode,
      the -o/--output argument can be used to specify a list of
      corresponding output files (which must be the same length). It
      is also possible to specify a format string to automatically
      generate file names. -o/--output defaults to "\1-\2.out" which is
      automatically expanded to "sampletag-toolname.out". The old
      positional arguments [IN] and [OUT] are maintained and allow for
      conveniently running the tools on a single sample file.
      [IN] is mutually exclusive with -i/--input and [OUT] is mutually
      exclusive with -o/--output. [OUT] now also accepts the filename
      format, but when not in batch mode, it still defaults to stdout.
      Note that by default, the sample tag is extracted from the input
      filenames by simply stripping the extension. This means a minimal
      batch processing command like "fdstools stuttermark -i *.csv"
      automatically creates a "...-stuttermark.out" file next to each
      CSV file in the current working directory.
    * Libconvert now also supports only specifying an output file.
      This makes it easier to write the default FDSTools library to a
      new file. E.g., "fdstools libconvert mynewfile.txt" now creates
      "mynewfile.txt" if it does not exist, and writes the default
      library to it. Most helpful.
bgcorrect.py 7.59 KB