# Get cBioPortal Variants ## Table of Contents * [get\_cbioportal\_variants](#get_cbioportal_variants) * [subset\_cpt](#subset_cpt) * [subset\_cst](#subset_cst) * [subset\_cna](#subset_cna) * [subset\_sv](#subset_sv) * [subset\_maf](#subset_maf) * [Sub-modules](#sub-modules) ## get\_cbioportal\_variants Requirement: * pandas * typing * typer * bed\_lookup() #### Example command ```bash python get_cbioportal_variants.py subset-maf --sid "Test1" --sid "Test2" --sid "Test3" ``` ```bash python get_cbioportal_variants.py subset-maf --ids /path/to/ids.txt ``` ```bash Usage: get_cbioportal_variants.py [OPTIONS] COMMAND [ARGS]... Options: --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. Commands: subset-cna Subset data_CNA.txt file for given set of sample ids. subset-cpt Subset data_clinical_patient.txt file for given set of patient... subset-cst Subset data_clinical_samples.txt file for given set of sample... subset-maf Subset MAF/TSV file and mark if an alteration is covered by... subset-sv Subset data_sv.txt file for given set of sample ids. ``` ### **subset\_cpt** ```bash Usage: get_cbioportal_variants.py subset-cpt [OPTIONS] Subset data_clinical_patient.txt file for given set of patient ids. Tool to do the following operations: A. Get subset of clinical information for samples based on PATIENT_ID in data_clinical_patient.txt file Requirement: pandas; typing; typer; bed_lookup(https://github.com/msk- access/python_bed_lookup) Options: -p, --cpt FILE Clinical Patient file generated by cBioportal repo [default: /work/access/production/resources/cbioportal/cur rent/msk_solid_heme/data_clinical_patient.txt] -i, --ids PATH List of ids to search for in the 'PATIENT_ID' column. Header of this file is 'sample_id' [default: ] --sid TEXT Identifiers to search for in the 'PATIENT_ID' column. Can be given multiple times [default: ] -n, --name TEXT Name of the output file [default: output_clinical_patient.txt] -c, --cname TEXT Name of the column header to be used for sub-setting [default: PATIENT_ID] --help Show this message and exit. ``` ### **subset\_cst** ```bash Usage: get_cbioportal_variants.py subset-cst [OPTIONS] Subset data_clinical_samples.txt file for given set of sample ids. Tool to do the following operations: A. Get subset of clinical information for samples based on SAMPLE_ID in data_clinical_sample.txt file Requirement: pandas; typing; typer; bed_lookup(https://github.com/msk- access/python_bed_lookup) Options: -s, --cst FILE Clinical Sample file generated by cBioportal repo [default: /work/access/production/resources/cbioportal/cur rent/msk_solid_heme/data_clinical_sample.txt] -i, --ids PATH List of ids to search for in the 'SAMPLE_ID' column. Header of this file is 'sample_id' [default: ] --sid TEXT Identifiers to search for in the 'SAMPLE_ID' column. Can be given multiple times [default: ] -n, --name TEXT Name of the output file [default: output_clinical_samples.txt] -c, --cname TEXT Name of the column header to be used for sub-setting [default: SAMPLE_ID] --help Show this message and exit. ``` ### **subset\_cna** ```bash Usage: get_cbioportal_variants.py subset-cna [OPTIONS] Subset data_CNA.txt file for given set of sample ids. Tool to do the following operations: A. Get subset of samples based on column header in data_CNA.txt file Requirement: pandas; typing; typer; bed_lookup(https://github.com/msk- access/python_bed_lookup) Options: -c, --cna FILE Copy Number Variant file generated by cBioportal repo [default: /work/access/production/resources/cbioportal/curr ent/msk_solid_heme/data_CNA.txt] -i, --ids PATH List of ids to search for in the 'header' of the file. Header of this file is 'sample_id' [default: ] --sid TEXT Identifiers to search for in the 'header' of the file. Can be given multiple times [default: ] -n, --name TEXT Name of the output file [default: output_CNA.txt] --help Show this message and exit. ``` ### **subset\_sv** ```bash Usage: get_cbioportal_variants.py subset-sv [OPTIONS] Subset data_sv.txt file for given set of sample ids. Tool to do the following operations: A. Get subset of structural variants based on Sample_ID in data_sv.txt file Requirement: pandas; typing; typer; bed_lookup(https://github.com/msk- access/python_bed_lookup) Options: -s, --sv FILE Structural Variant file generated by cBioportal repo [default: /work/access/production/resources/cbioportal/cur rent/msk_solid_heme/data_sv.txt] -i, --ids PATH List of ids to search for in the 'Sample_ID' column. Header of this file is 'sample_id' [default: ] --sid TEXT Identifiers to search for in the 'Sample_ID' column. Can be given multiple times [default: ] -n, --name TEXT Name of the output file [default: output_sv.txt] -c, --cname TEXT Name of the column header to be used for sub-setting [default: Sample_ID] --help Show this message and exit. ``` ### **subset\_maf** ```bash Usage: get_cbioportal_variants.py subset-maf [OPTIONS] Subset MAF/TSV file and mark if an alteration is covered by BED file or not Tool to do the following operations: A. Get subset of variants based on Tumor_Sample_Barcode in data_mutations_extended.txt file B. Mark the variants as overlapping with BED file as covered [yes/no], by appending "covered" column to the subset MAF Requirement: pandas; typing; typer; bed_lookup(https://github.com/msk- access/python_bed_lookup) Options: -m, --maf FILE MAF file generated by cBioportal repo [default: /work/acc ess/production/resources/cbioportal/current/msk_solid_heme /data_mutations_extended.txt] -i, --ids PATH List of ids to search for in the 'Tumor_Sample_Barcode' column. Header of this file is 'sample_id' [default: ] --sid TEXT Identifiers to search for in the 'Tumor_Sample_Barcode' column. Can be given multiple times [default: ] -b, --bed FILE BED file to find overlapping variants [default: /work/access/production/resources/msk- access/current/regions_of_interest/current/MSK- ACCESS-v1_0-probe-A.sorted.bed] -n, --name TEXT Name of the output file [default: output.maf] -c, --cname TEXT Name of the column header to be used for sub-setting [default: Tumor_Sample_Barcode] --help Show this message and exit. ``` ### Sub-modules #### **read\_tsv** ```python def read_tsv(tsv) ``` Read a tsv file **Arguments**: * `maf` *File* - Input MAF/tsv like format file **Returns**: * `data_frame` - Output a data frame containing the MAF/tsv #### **read\_ids** ```python def read_ids(sid, ids) ``` make a list of ids **Arguments**: * `sid` *tuple* - Multiple ids as tuple * `ids` *File* - File containing multiple ids **Returns**: * `list` - List containing all ids #### **filter\_by\_columns** ```python def filter_by_columns(sid, tsv_df) ``` Filter data by columns **Arguments**: * `sid` *list* - list of columns to subset over * `tsv_df` *data\_frame* - data\_frame to subset from **Returns**: * `data_frame` - A copy of the subset of the data\_frame #### **filter\_by\_rows** ```python def filter_by_rows(sid, tsv_df, col_name) ``` Filter the data by rows **Arguments**: * `sid` *list* - list of row names to subset over * `tsv_df` *data\_frame* - data\_frame to subset from * `col_name` *string* - name of the column to filter using names in the sid **Returns**: * `data_frame` - A copy of the subset of the data\_frame #### **read\_bed** ```python def read_bed(bed) ``` Read BED file using bed\_lookup **Arguments**: * `bed` *file* - File ins BED format to read **Returns**: object : bed file object to use for filtering #### **check\_if\_covered** ```python def check_if_covered(bedObj, mafObj) ``` Function to check if a variant is covered in a given bed file **Arguments**: * `bedObj` *object* - BED file object to check coverage * `mafObj` *data\_frame* - data frame to check coverage against coordinates using column 'Chromosome' and position column is 'Start\_Position' **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 --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://cmo-ci.gitbook.io/cmo-access-data-analysis/miscellaneous-utility-scripts/get-cbioportal-variants.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.