Convert CSV to MAF
Convert output of Rscript (filter_calls.R) CSV file to MAF
The Tool does the following operations:
Read one or more files from the inputs
Removes unwanted columns, modifying the column headers depending on the requirements
Massaging the data frame to make it compatible with MAF format
Write the data frame to a file in MAF format and Excel format
Requirements
Example command
Explicitly specifying files on command line
python csv_to_maf.py -i /path/to/Test1.csv -i /path/to/Test2.csv -i /path/to/Test3.csv
Specifying files in a text FileOfFiles
python csv_to_maf.py -l /path/to/FileOfFiles.txt
where FileOfFiles.txt
> cat FileOfFiles.txt
/path/to/Test1.csv
/path/to/Test2.csv
/path/to/Test3.csv
Keeping normal samples identified using "normal" string, by default they are filtered
python csv_to_maf.py -n -i /path/to/Test1.csv -i /path/to/Test2.csv -i /path/to/Test3.csv
# OR
python csv_to_maf.py -n -l /path/to/FileOfFiles.txt
Usage
> python csv_to_maf.py --help
Usage: csv_to_maf.py [OPTIONS]
Tool does the following operations:
A. Read one or more files from the inputs
B. Removes unwanted columns, modifying the column headers depending on the
requirements
C. Massaging the data frame to make it compatible with MAF format
D. Write the data frame to a file in MAF format and Excel format
Requirement: pandas; openpyxl; typing; typer;
Options:
-l, --list PATH File of files, List of CSV files to be
converted to maf, one per line, no header,
CSV file generated by Rscript filter_calls.R
[default: ]
-i, --csv FILE File to convert from csv to maf. CSV file
generated by Rscript filter_calls.R, Can be
given multiple times [default: ]
-n, --normal / -N, --keep-normal
Keep samples tagged as normal [default:
False]
-p, --prefix TEXT Prefix of the output MAF and EXCEL file
[default: csv_to_maf_output]
--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.