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alitv-filter.md

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NAME

AliTV filter - filters AliTV JSON files for postprocessing

SYNOPSIS

# Filter input file based on settings in JSON
alitv-filter.pl --input in.json --output out.json

# Filter input file based on settings in JSON in combination with
# the command line settings
alitv-filter.pl --input in.json --output out2.json --min-link-length 10000 --min-link-identity 90%

# Filter input file based on the command line settings and ignoring
# JSON settings
alitv-filter.pl --input in.json --output out3.json --ignore-json --min-link-length 10000 --min-link-identity 90%

DESCRIPTION

The script filters AliTV JSON files for postprocessing.

OPTIONS

  • --help|?|man Help

    Shows description of this program, its usage, and its parameters/options.

  • --input Input file

    The name of the input file. Default value is input from STDIN which can be manually enabled by --input -.

  • --output Output file

    The name of the output file. Default value is output to STDOUT which can be manually enabled by --output -.

  • --min-link-identity/--max-lin-identity Minimum/Maximum identity for Links

    Specifies the minimal or maximum identity value for links. A float is expected. Numbers greater than 1 will be handled as percentage values, values up to 1.0 will be multiplied by 100 due to a fraction instead of a percentage value is assumed.

  • --min-link-length/--max-link-length Minimum/Maximum length for Links

    Specifies the minimal or maximum length for links. A integer is expected and specifies the length in nucleotids.

  • --min-seq-length/--max-seq-length Minimum/Maximum length for chromosomes

    Specifies the minimal or maximum length for chromosomes. An integer is expected and specifies the length in nucleotids.

  • --ignore-json Ignore settings in JSON file

    If enabled, the current settings from the JSON are ignored, otherwise a combination of the limits inside the JSON file and the command line parameters will be used for filtering.

AUTHOR

Frank Förster <[email protected]>

SEE ALSO