ParseLog¶
Parses records in the console log of pRESTO modules
usage: ParseLog [--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.