NAME

ParseLog.py - Parses records in the console log of pRESTO modules

DESCRIPTION

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.

AUTHOR


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