This script enables to run the create_report.R script on multiple patients
template_path Path, optional - "Path to the template.Rmd or template_days.Rmd to be used with create_report.R when --repo is not given".template_path pathlib.Path, optional - Path to template RMarkdown file. Defaults to None.sample_idaccess_data_analysis=>0.1.2 # works with this repo tag
typer==0.3.2
typing_extensions==3.10.0.0
pandas==1.2.5
rich==12.1.0Usage: run_create_report.py [OPTIONS]
Options:
-r, --repo PATH Base path to where the git repository is
located for access_data_analysis
-s, --script PATH Path to the create_report.R script, fall
back if `--repo` is not given
-t, --template PATH Path to the template.Rmd or
template_days.Rmd to be used with
create_report.R when `--repo` is not given
-m, --manifest FILE File containing meta information per sample.
Require following columns in the header:
cmo_patient_id, sample_id, dmp_patient_id,
collection_date or collection_day,
timepoint. If dmp_sample_id column is given
and has information that will be used to run
facets. If dmp_sample_id is not given and
dmp_patient_id is given than it will be used
to get the Tumor sample with lowest number.
If dmp_sample_id or dmp_patient_id is not
given then it will run without the facet maf
file [required]
-v, --variant-results DIRECTORY
Base path for all results of small variants
as generated by filter_calls.R script in
access_data_analysis (Make sure only High
Confidence calls are included) [required]
-c, --cnv-results DIRECTORY Base path for all results of CNV as
generated by CNV_processing.R script in
access_data_analysis [required]
-f, --facet-repo DIRECTORY Base path for all results of facets on
Clinical MSK-IMPACT samples [default: /juno
/work/ccs/shared/resources/impact/facets/all
/]
-bf, --best-fit If this is set to True then we will attempt
to parse `facets_review.manifest` file to
pick the best fit for a given dmp_sample_id
[default: False]
-l, --tumor-type TEXT Tumor type label for the report [required]
-cfm, --copy-facet-maf If this is set to True then we will copy the
facet maf file in the directory specified in
`copy_facet_dir` [default: False]
-cfd, --copy-facet-dir PATH Directory path where the facet maf file
should be copied.
-d, --template-days If the `--repo` option is specified and if
this is set to True then we will use the
template_days RMarkdown file as the template
[default: False]
-gm, --generate-markdown If given, the create_report.R will be run
with `-md` flag to generate markdown
[default: False]
-ff, --force If this is set to True then we will not stop
if an error is encountered in a given sample
while running create_report.R but keep on
running for the next sample [default:
False]
--install-completion Install completion for the current shell.
--show-completion Show completion for the current shell, to
copy it or customize the installation.
--help Show this message and exit.> python python/run_create_report/run_create_report.py \
-m /home/shahr2/bergerlab/Project_10619_D/small_variants/manifest_noDate_days.tsv \
-r /home/shahr2/github/access_data_analysis \
-v /home/shahr2/bergerlab/Project_10619_D/small_variants/results_20Jan2023/results_stringent/ \
-c /home/shahr2/bergerlab/Project_10619_D/small_variants/results_20Jan2023/CNA_final_call_set \
-l "Melanoma" -gm -d -cfm -ff -bf> python python/run_create_report/run_create_report.py \
-m /home/shahr2/bergerlab/Project_10619_D/small_variants/manifest_noDate_days.tsv \
-r /home/shahr2/github/access_data_analysis \
-v /home/shahr2/bergerlab/Project_10619_D/small_variants/results_20Jan2023/results_stringent/ \
-c /home/shahr2/bergerlab/Project_10619_D/small_variants/results_20Jan2023/CNA_final_call_set \
-l "Melanoma" -gm -ffdef check_required_columns(manifest, template_days=None)def generate_repo_path(repo_path=None, script_path=None, template_path=None, template_days=None)def read_manifest(manifest)def get_row(tsv_file)def get_small_variant_csv(patient_id, csv_path)def run_cmd(cmd)def run_multiple_cmd(commands, parallel_process=None)def generate_facet_maf_path(facet_path, patient_id, sample_id=None)def get_maf_path(maf_path, patient_id, sample_id)def get_best_fit_folder(facet_manifest_path)def generate_create_report_cmd(script, markdown, template_file, cmo_patient_id, csv_file, manifest, cnv_path, dmp_patient_id, dmp_sample_id, dmp_facet_maf, tumor_type=None)