Fix #127 - update examples

[dnil]

Description

Fixed

• documentation examples

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_[TOOL]-t [TOOL] -b [THIS-BRANCH-NAME] -a

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[fellen31]

LGTM! We can look into changing --whole_gene separately.

[fellen31]

Is -g/--whole_gene still relevant or deprecated?

[dnil]

It indeed looks beyond deprecated: completely unused nowadays.

[dnil]

As far as I can tell, it was removed functionally with #77.

[dnil]

I noted that MIP still has support for the --whole-gene so I left it there again. It would formally be a major bump when it goes. Let's synk that with something that really needs doing. I marked it more clearly so we don't loose it again.

(genmod) ➜  genmod git:(fix_doc_examples) ✗ genmod models --help
Usage: genmod models [OPTIONS] <vcf_file> or -

  Annotate genetic models for vcf variants.

  Checks what patterns of inheritance that are followed in a VCF file. The
  analysis is family based so each family that are specified in the family
  file and exists in the variant file will get it's own annotation.

  Note that the "whole_gene" flag has been disabled and will be removed in a
  later version.

Options:
  -f, --family_file <ped_file>
  -t, --family_type [ped|alt|cmms|mip]
                                  If the analysis use one of the known setups,
                                  please specify which one.
  -r, --reduced_penetrance, --reduced-penetrance <tsv_file>
                                  File with gene ids that have reduced
                                  penetrance.
  --vep                           If variants are annotated with the Variant
                                  Effect Predictor.
  --phased                        If data is phased use this flag.
  -s, --strict                    If strict model annotations should be
                                  used(see documentation).
  -w, --whole_gene, --whole-gene  DEPRECATED FLAG - on by default
  -p, --processes INTEGER         Define how many processes that should be use
                                  for annotation.
  -s, --silent                    Do not print the variants.
  -k, --keyword TEXT              What annotation keyword that should be used
                                  when  searching for features.
  -o, --outfile FILENAME          Specify the path to a file where results
                                  should be stored.
  --temp_dir PATH                 Path to tempdir
  --help                          Show this message and exit.