ParseLog.py
Parses records in the console log of pRESTO modules
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 ...]
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -o <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).
- --outdir <out_dir>
Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
- --outname <out_name>
Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
- --delim <delimiter>
A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
- -l <record_files>
List of log files to parse.
- -f <fields>
List of fields to collect. The sequence identifier may be specified using the hidden field name “ID”.
- output files:
- table
tab delimited table of the selected annotations.
- output annotation fields:
- <user defined>
annotation fields specified by the -f argument.