Voila


TSV

VOILA provides a tab-delimited text file to allow users to parse MAJIQ results and further analyze particular LSVs or genes of interest. Most fields are shared between single PSI and delta PSI computations for the expected values and the confidence measures (variance in the case of single PSI and the probability of |delta psi| > 0.2 (or your specified alternative threshold) in delta PSI analysis). The common fields are: Gene name; LSV ID; LSV Type; LSV attributes (A5SS, A3SS, ES, Num. Junctions and Num. Exons); chromosome; strand; LSV coordinates (junctions and exons coordinates); and finally, if additional evidence is required to determine what is the start/end of an LSV, a list with all possible alternative starts and ends is provided.

Usage

The usage statement for voila tsv --help is the following:

usage: voila tsv [-h] -f FILE_NAME [--threshold THRESHOLD]
[--non-changing-threshold NON_CHANGING_THRESHOLD]
[--probability-threshold PROBABILITY_THRESHOLD] [--show-all]
[--lsv-types-file LSV_TYPES]
[--lsv-types [LSV_TYPES [LSV_TYPES ...]]]
[--lsv-ids-file LSV_IDS] [--lsv-ids [LSV_IDS [LSV_IDS ...]]]
[--gene-names-file GENE_NAMES]
[--gene-names [GENE_NAMES [GENE_NAMES ...]]]
[--gene-ids-file GENE_IDS]
[--gene-ids [GENE_IDS [GENE_IDS ...]]] [-j NPROC] [--debug]
[-l LOGGER] [--silent]
files [files ...]
positional arguments:
files List of files or directories which contains the splice
graph and voila files.
optional arguments:
-h, --help show this help message and exit
--threshold THRESHOLD
Filter out LSVs with no junctions predicted to change
over a certain value. Even when show-all is used this
value is still used to calculate the probability in
the TSV. The default is "0.2".
--non-changing-threshold NON_CHANGING_THRESHOLD
The default is "0.05".
--probability-threshold PROBABILITY_THRESHOLD
This is off by default.
--show-all Show all LSVs including those with no junction with
significant change predicted.
--lsv-types-file LSV_TYPES
Location of file that contains a list of LSV types
which should remain in the results. One type per line
--lsv-types [LSV_TYPES [LSV_TYPES ...]]
LSV types which should remain in the results
--lsv-ids-file LSV_IDS
Location of file that contains a list of LSV IDs which
should remain in the results. One ID per line.
--lsv-ids [LSV_IDS [LSV_IDS ...]]
LSV IDs, separated by spaces, which should remain in
the results. e.g LSV_ID1 LSV_ID2 ...
--gene-names-file GENE_NAMES
Location of file that contains a list of common gene
names which should remain in the results. One name per
line.
--gene-names [GENE_NAMES [GENE_NAMES ...]]
Common gene names, separated by spaces, which should
remain in the results. e.g. GENE1 GENE2 ...
--gene-ids-file GENE_IDS
Location of file that contains a list of gene IDs
which should remain in the results. One name per line.
--gene-ids [GENE_IDS [GENE_IDS ...]]
Gene IDs, separated by spaces, which should remain in
the results. e.g. GENE_ID1 GENE_ID2 ...
-j NPROC, --nproc NPROC
Number of processes used to produce output. Default is
half of system processes.
--debug
-l LOGGER, --logger LOGGER
Set log file and location. There will be no log file
if not set.
--silent Do not write logs to standard out.
required named arguments:
-f FILE_NAME, --file-name FILE_NAME
Set the TSV file's name and location.

Example

For the voila command you will have to supply a filename for the tsv. Again, psi or deltapsi will be detected from the voila file supplied. `A sample command for voila tsv would be something similar to:

$ voila tsv splicegraph.sql psi.voila -f output_file.tsv