LTA’s Parser
The root lta parser.
For a detailed description of the tool and how to use it, please see the README. A short overview is given here.
The location of the input data file is the first positional argument,
while the location to which the output files should be saved is the second positional.
The “0” threshold is specified with option -t/--threshold.
This should be passed as a floating point number between 0 and 1, inclusive.
If it is not provided,
then a default of 0.3 is used.
The number of bootstrap replicates to use for estimating the p-values
can be specified with -b/--boot-reps.
Generally, higher repetitions increases accuracy,
A deault of 1000 is used to provide a balance between speed and accuracy.
Many calculations are dependent on knowing where certain metadata is stored.
Namely, the experimental conditions (specified with --group),
the compartment of origin (specified with --compartment),
the sample ID (specified with --sample-id),
and the lipidomics mode (specifed with --mode).
If these are not passed,
then they default to “Group”, “Compartment”, “SampleID”, and “Mode” respectively.
We also have to know how many rows of metadata there are.
This is specified with --n-rows-metadata,
and defaults to 11 if not given.
The error-normalised fold change (ENFC) calculation must know the labels for
experimental and control group.
Without this knowledge,
the concept of fold change is meaningless.
To specify, pass --control control.
Every condition specified in Group will then be divided by control
to calculate the ENFC for all conditions.
Finally,
all options can be passed in an config file.
This file expects values of the format option=value.
By default,
the CLI looks for lta_conf.txt,
though any file can be specified with the -c/--config flag.
Values in the config file override the defaults,
and values passed to the CLI override the config file.
Like all good CLIs,
-V returns the version while -h/--help returns help.
- lta.parser.lta_parser
The argument parser for the root command.
- Type
argparse.ArgumentParser