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>

HTML

Usage

usage: voila view [-h] [-p PORT] [--force-index] [-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
  -p PORT, --port PORT  Set service port. Default is a random.
  --force-index         Create index even if already exists.
  -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.


Example

voila view <location of splice graph file> <location of voila file>