ParseLog.py(1)

ParseLog.py1

Parses records in the console log of presto modules

Overview

usage: ParseLog.py [--version] [-h] [-o OUT_FILES [OUT_FILES ...]]

[--outdir OUT_DIR] [--outname OUT_NAME] [--delim DELIMITER DELIMITER DELIMITER] -l RECORD_FILES [RECORD_FILES ...] -f FIELDS [FIELDS ...]

Parses records in the console log of pRESTO modules

help:

--version

show program's version number and exit

-h, --help

show this help message and exit

standard arguments:

-o OUT_FILES [OUT_FILES ...]

Explicit output file name(s). Note, this argument cannot be used with the --failed, --outdir, or --outname arguments. If unspecified, then the output filename will be based on the input filename(s). (default: None)

--outdir OUT_DIR

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified. (default: None)

--outname OUT_NAME

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files. (default: None)

--delim DELIMITER DELIMITER DELIMITER

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively. (default: ('|', '=', ','))

parsing arguments:

-l RECORD_FILES [RECORD_FILES ...]

List of log files to parse. (default: None)

-f FIELDS [FIELDS ...]

List of fields to collect. The sequence identifier may be specified using the hidden field name "ID". (default: None)

output files:

table

tab delimited table of the selected annotations.

output annotation fields:

<user defined>

annotation fields specified by the -f argument.

Releases

Unchanged in 3 releases since Debian 11 (Bullseye).

  1. 11–13

Author

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.

From presto 0.7.2-2 in Debian 13 (Trixie). Parsed by carta from the page's man source.