# 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