Command line reference

This section contains the exhaustive list of the sub-commands and options available for JASS on the command line.

usage: jass [-h]
            {serve,list-phenotypes,create-project-data,clean-project-data,create-inittable,create-worktable,plot-manhattan,qq-plot,plot-quadrant,add-gene-annotation,extract-tsv,predict-gain}
            ...

Positional Arguments

action: Possible choices: serve, list-phenotypes, create-project-data, clean-project-data, create-inittable, create-worktable, plot-manhattan, qq-plot, plot-quadrant, add-gene-annotation, extract-tsv, predict-gain

Sub-commands

serve

run JASS web server

jass serve [-h]

list-phenotypes

list phenotypes available in a data file

jass list-phenotypes [-h] [--init-table-path INIT_TABLE_PATH]

Named Arguments

--init-table-path

path to the initial data file, default is the configured path (JASS_DATA_DIR/initTable.hdf5)

Default: "/builds/statistical-genetics/jass-server/data/initTable.hdf5"

create-project-data

compute joint statistics and generate plots for a given set of phenotypes

jass create-project-data [-h] [--init-table-path INIT_TABLE_PATH] --phenotypes
                         PHENOTYPES [PHENOTYPES ...] --worktable-path
                         WORKTABLE_PATH [--remove-nans]
                         [--manhattan-plot-path MANHATTAN_PLOT_PATH]
                         [--quadrant-plot-path QUADRANT_PLOT_PATH]
                         [--zoom-plot-path ZOOM_PLOT_PATH]
                         [--qq-plot-path QQ_PLOT_PATH]
                         [--significance-treshold SIGNIFICANCE_TRESHOLD]
                         [--post-filtering POST_FILTERING]
                         [--custom-loadings CUSTOM_LOADINGS]
                         [--chunk-size CHUNK_SIZE]
                         [--csv-file-path CSV_FILE_PATH]
                         [--chromosome-number CHROMOSOME_NUMBER]
                         [--start-position START_POSITION]
                         [--end-position END_POSITION]
                         [--omnibus | --sumz | --fisher_test | --meta_analysis]

Named Arguments

--init-table-path

path to the initial data file, default is the configured path (JASS_DATA_DIR/initTable.hdf5)

Default: "/builds/statistical-genetics/jass-server/data/initTable.hdf5"

--phenotypes

list of selected phenotypes

--worktable-path

path to the worktable file to generate

--remove-nans

Default: False

--manhattan-plot-path

path to the genome-wide manhattan plot to generate

--quadrant-plot-path

path to the quadrant plot to generate

--zoom-plot-path

path to the local plot to generate

--qq-plot-path

path to the quantile-quantile plot to generate

--significance-treshold

The treshold at which a p-value is considered significant

Default: 5e-08

--post-filtering

If a filtering to remove outlier will be applied (in this case the result of SNPs considered aberant will not appear in the worktable)

Default: True

--custom-loadings

path toward a csv file containing custom loading for sumZ tests

--chunk-size

Number of region to load in memory at once

Default: 50

--csv-file-path

path to the results file in csv format

--chromosome-number

option used only for local analysis: chromosome number studied

--start-position

option used only for local analysis: start position of the region studied

--end-position

option used only for local analysis: end position of the region studied

--omnibus

Default: True

--sumz

Default: False

--fisher_test

Default: False

--meta_analysis

Default: False

clean-project-data

Remove old projects data that haven't been accessed recently

jass clean-project-data [-h]
                        [--max-days-without-access MAX_DAYS_WITHOUT_ACCESS]

Named Arguments

--max-days-without-access

A project is marked for large file deletion if the number of days elapsed since the last access is greater than the amount provided.

Default: 30

create-inittable

import data into an initial data file

jass create-inittable [-h] --input-data-path INPUT_DATA_PATH
                      [--init-covariance-path INIT_COVARIANCE_PATH]
                      --regions-map-path REGIONS_MAP_PATH
                      --description-file-path DESCRIPTION_FILE_PATH
                      [--init-table-path INIT_TABLE_PATH]
                      [--init-genetic-covariance-path INIT_GENETIC_COVARIANCE_PATH]
                      [--init-table-metadata-path INIT_TABLE_METADATA_PATH]

Named Arguments

--input-data-path

path to the GWAS data file (ImpG format) to import. the path must be specify between quotes

--init-covariance-path

path to the covariance file to import

--regions-map-path

path to the genome regions map (BED format) to import

--description-file-path

path to the GWAS studies metadata file

--init-table-path

path to the initial data file to produce, default is the configured path (JASS_DATA_DIR/initTable.hdf5)

Default: "/builds/statistical-genetics/jass-server/data/initTable.hdf5"

--init-genetic-covariance-path

path to the genetic covariance file to import. Used only for display on Jass web application

--init-table-metadata-path

path to metadata file to attache to the initial data file

create-worktable

compute joint statistics for a given set of phenotypes

jass create-worktable [-h] [--init-table-path INIT_TABLE_PATH] --phenotypes
                      PHENOTYPES [PHENOTYPES ...] --worktable-path
                      WORKTABLE_PATH
                      [--significance-treshold SIGNIFICANCE_TRESHOLD]
                      [--post-filtering POST_FILTERING]
                      [--custom-loadings CUSTOM_LOADINGS]
                      [--csv-file-path CSV_FILE_PATH]
                      [--chunk-size CHUNK_SIZE] [--remove-nans]
                      [--chromosome-number CHROMOSOME_NUMBER]
                      [--start-position START_POSITION]
                      [--end-position END_POSITION]
                      [--omnibus | --sumz | --fisher_test | --meta_analysis]

Named Arguments

--init-table-path

path to the initial data table, default is the configured path (JASS_DATA_DIR/initTable.hdf5)

Default: "/builds/statistical-genetics/jass-server/data/initTable.hdf5"

--phenotypes

list of selected phenotypes

--worktable-path

path to the worktable file to generate

--significance-treshold

threshold at which a p-value is considered significant

Default: 5e-08

--post-filtering

If a filtering to remove outlier will be applied (in this case the result of SNPs considered aberant will not appear in the worktable)

Default: True

--custom-loadings

path toward a csv file containing custom loading for sumZ tests

--csv-file-path

path to the results file in csv format

--chunk-size

Number of region to load in memory at once

Default: 50

--remove-nans

Default: False

--chromosome-number

option used only for local analysis: chromosome number studied

--start-position

option used only for local analysis: start position of the region studied

--end-position

option used only for local analysis: end position of the region studied

--omnibus

Default: True

--sumz

Default: False

--fisher_test

Default: False

--meta_analysis

Default: False

plot-manhattan

generate genome-wide manhattan plot for a given set of phenotypes

jass plot-manhattan [-h] --worktable-path WORKTABLE_PATH --plot-path PLOT_PATH

Named Arguments

--worktable-path: path to the worktable file containing the data
--plot-path: path to the manhattan plot file to generate

qq-plot

generate genome-wide qqplot of p value. Warning : require a lot of memory

jass qq-plot [-h] --worktable-path WORKTABLE_PATH --plot-path PLOT_PATH

Named Arguments

--worktable-path: path to the worktable file containing the data
--plot-path: path to the manhattan plot file to generate

plot-quadrant

generate a quadrant plot for a given set of phenotypes

jass plot-quadrant [-h] --worktable-path WORKTABLE_PATH --plot-path PLOT_PATH
                   [--significance-treshold SIGNIFICANCE_TRESHOLD]

Named Arguments

--worktable-path

path to the worktable file containing the data

--plot-path

path to the quadrant plot file to generate

--significance-treshold

threshold at which a p-value is considered significant

Default: 5e-08

add-gene-annotation

add information about genes ansd exons to the inittable

jass add-gene-annotation [-h] --gene-data-path GENE_DATA_PATH
                         --init-table-path INIT_TABLE_PATH
                         [--gene-csv-path GENE_CSV_PATH]
                         [--exon-csv-path EXON_CSV_PATH]

Named Arguments

--gene-data-path: path to the GFF file containing gene and exon data
--init-table-path: path to the initial table file to update
--gene-csv-path: path to the file df_gene.csv
--exon-csv-path: path to the file df_exon.csv

extract-tsv

Extract a table from a hdf5 repository to the tsv format. Will work for the worktables and the inittable. WARNING: can strongly increase storage space needed

jass extract-tsv [-h] --hdf5-table-path HDF5_TABLE_PATH --tsv-path TSV_PATH
                 [--table-key TABLE_KEY]

Named Arguments

--hdf5-table-path: path to the worktable file containing the data
--tsv-path: path to the tsv table
--table-key: Existing key are 'SumStatTab' : The results of the joint analysis by SNPs - 'PhenoList' : the meta data of analysed GWAS - 'COV' : The H0 covariance used to perform joint analysis - 'GENCOV' (If present in the initTable): The genetic covariance as computed by the LDscore. Uniquely for the worktable: 'Regions' : Results of the joint analysis summarised by LD regions (Notably Lead SNPs by regions) - 'summaryTable': a double entry table summarizing the number of significant regions by test (univariate vs joint test)

predict-gain

Predict gain based on the genetic architecture of the set of multi-trait. To function, this command need the inittable to contain genetic covariance store under the key 'GEN_COV in the inittable'

jass predict-gain [-h] --inittable-path INITTABLE_PATH --combination-path
                  COMBINATION_PATH --gain-path GAIN_PATH

Named Arguments

--inittable-path: Path to the inittable
--combination-path: Path to the file storing combination to be scored
--gain-path: path to save predicted gain

Utilities

usage: scripts/hdf5_add_attributes [-h] --init-table-path HDF5_FILE
                                   [--init-table-metadata-path INIT_TABLE_METADATA_PATH | --clean-metadata]
                                   [--title TITLE] [--description DESCRIPTION]
                                   [--ancestry ANCESTRY] [--assembly ASSEMBLY]

Named Arguments

--init-table-path

path to the inittable to edit

--init-table-metadata-path

path to metadata file to attache to the inittable. Note that all previous metadata are purged.

--clean-metadata

Remove all information in metadata before adding new one

Default: False

--title

title to append to the metadata

--description

description to append to the metadata

--ancestry

ancestry to append to the metadata

--assembly

assembly to append to the metadata