Voila

TSV

Usage

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

voila tsv <location of splice graph file> <location of voila file> -f <location and name of tsv file>

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