> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/cmo-access-data-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/cmo-access-data-analysis/run-create_report.r.md). # Run create\_report.R * [Requirements](#requirements) * [run\_create\_report](#run_create_report) * [Main Script (run\_create\_report.py)](#main-script-run_create_report.py) * [Submodules](#submodules) ## Requirements ```bash access_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==12.1.0 ``` ## run\_create\_report ### Main Script (run\_create\_report.py) ```bash Usage: 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. ``` Wrapper script to run create\_report.R **Arguments**: * `repo_path` *Path, optional* - "Base path to where the git repository is located for access\_data\_analysis". * `script_path` *Path, optional* - "Path to the create\_report.R script, fall back if `--repo` is not given". * `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". * `manifest` *Path, required* - "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". * `variant_path` *Path, required* - "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)". * `cnv_path` *Path, required* - "Base path for all results of CNV as generated by CNV\_processing.R script in access\_data\_analysis". * `facet_repo` *Path, required* - "Base path for all results of facets on Clinical MSK-IMPACT samples". * `best_fit` *bool, optional* - "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". * `tumor_type` *str, required* - "Tumor type label for the report". * `copy_facet` *bool, optional* - "If this is set to True then we will copy the facet maf file in the directory specified in `copy_facet_dir`". * `copy_facet_dir` *Path, optional* - "Directory path where the facet maf file should be copied.". * `template_days` *bool, optional* - "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". * `markdown` *bool, optional* - "If given, the create\_report.R will be run with `-md` flag to generate markdown". * `force` *bool, optional* - "If this is set to True then we will not stop if an error is encountered in a given sample but keep on running for the next sample". #### **Usage** * Using Generate Markdown, copy facet maf file, use template\_days RMarkdown, force flag and best fit for facets ```bash > 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 ``` * Using Generate Markdown, force flag and default fit for facets ```bash > 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 -ff ``` ## Submodules ### check\_required\_columns #### check\_required\_columns ```python def check_required_columns(manifest, template_days=None) ``` Check if all required columns are present in the sample manifest file **Arguments**: * `manifest` *data\_frame* - meta information file with information for each sample * `template_days` *bool* - True|False if template days RMarkdown will be used **Raises**: * `typer.Abort` - if "cmo\_patient\_id" column not provided * `typer.Abort` - if "cmo\_sample\_id/sample\_id" column not provided * `typer.Abort` - if "dmp\_patient\_id" column not provided * `typer.Abort` - if "collection\_date/collection\_day" column not provided * `typer.Abort` - if "timepoint" column not provided **Returns**: * `list` - column name for the manifest file * `data_frame` - data\_frame with unique ids to traverse over ### generate\_repo\_paths #### generate\_repo\_path ```python def generate_repo_path(repo_path=None, script_path=None, template_path=None, template_days=None) ``` Generate path to create\_report.R and template RMarkdown file **Arguments**: * `repo_path` *pathlib.Path, optional* - Path to clone of git repo access\_data\_analysis. Defaults to None. * `script_path` *pathlib.Path, optional* - Path to create\_report.R. Defaults to None. * `template_path` *pathlib.Path, optional* - Path to template RMarkdown file. Defaults to None. * `template_days` *bool, optional* - True|False to use days template if using repo\_path. Defaults to None. **Raises**: * `typer.Abort` - Abort if both repo\_path and script\_path are not given * `typer.Abort` - Abort if both repo\_path and template\_path are not given **Returns**: * `str` - Path to create\_report.R and path to template markdown file ### read\_manifest #### read\_manifest ```python def read_manifest(manifest) ``` Read manifest file **Arguments**: * `manifest` *pathlib.PATH* - *description* **Returns**: * `data_frame` - *description* #### get\_row ```python def get_row(tsv_file) ``` Function to skip rows **Arguments**: * `tsv_file` *file* - file to be read **Returns**: * `list` - lines to be skipped ### get\_small\_variant\_csv #### get\_small\_variant\_csv ```python def get_small_variant_csv(patient_id, csv_path) ``` Get the path to CSV file to be used for a given patient containing all variants **Arguments**: * `patient_id` *str* - patient id used to identify the csv file * `csv_path` *pathlib.path* - base path where the csv file is expected to be present **Raises**: * `typer.Abort` - if no csv file is returned * `typer.Abort` - if more then one csv file is returned **Returns**: * `str` - path to csv file containing the variants ### run\_cmd #### run\_cmd ```python def run_cmd(cmd) ``` Given a system command run it using subprocess **Arguments**: * `cmd` *str* - System command to be run as a string #### run\_multiple\_cmd ```python def run_multiple_cmd(commands, parallel_process=None) ``` Given a system command run it using subprocess **Arguments**: * `cmd` *list\[str]* - list of system commands to be run ### generate\_facet\_maf\_path #### generate\_facet\_maf\_path ```python def generate_facet_maf_path(facet_path, patient_id, sample_id=None) ``` Get path of maf associated with facet-suite output **Arguments**: * `facet_path` *pathlib.PATH|str* - path to search for the facet file * `patient_id` *str* - patient id to be used to search, default is set to None * `sample_id` *str* - sample id to be used to search, default is set to None **Returns**: * `str` - path of the facets maf #### get\_maf\_path ```python def get_maf_path(maf_path, patient_id, sample_id) ``` Get the path to the maf file **Arguments**: * `maf_path` *pathlib.Path* - Base path of the maf file * `patient_id` *str*: DMP Patient ID for facets * `sample_id` *str* - DMP Sample ID if any for facets **Returns**: * `str` - Path to the maf file #### get\_best\_fit\_folder ```python def get_best_fit_folder(facet_manifest_path) ``` Get the best fit folder for the given facet manifest path **Arguments**: * `facet_manifest_path` *str* - manifest path to be used for determining best fit **Returns**: * `pathlib.Path` - path to the folder containing best fit maf files ### generate\_create\_report\_cmd #### generate\_create\_report\_cmd ```python 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) ``` Create the system command that should be run for create\_report.R **Arguments**: * `script` *str* - path for create\_report.R * `markdown` *bool* - True|False to generate markdown output * `template_file` *str* - path for the template file * `cmo_patient_id` *str* - patient id from CMO * `csv_file` *str* - path to csv file containing variant information * `tumor_type` *str* - tumor type label * `manifest` *pathlib.Path* - path to the manifest containing meta data * `cnv_path` *pathlib.Path* - path to directory having cnv files * `dmp_patient_id` *str* - patient id of the clinical msk-impact sample * `dmp_sample_id` *str* - sample id of the clinical msk-impact sample * `dmp_facet_maf` *str* - path to the clinical msk-impact maf file annotated for facets results **Returns**: * `cmd` *str* - system command to run for create\_report.R * `html_output` *pathlib.Path* - where the output file should be written --- # Agent Instructions This documentation is published with GitBook. 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