cmapBQ.utils package

Module contents

cmapBQ.utils.csv_to_gctx(filepaths, outpath, use_gctx=True)

Convert list of csv files to gctx. CSVs must have ‘rid’, ‘cid’ and ‘value’ columns No other columns or metadata is preserved.

Parameters

• filepaths – List of paths to CSVs

• outpath – output directory of file

• use_gctx – use GCTX HDF5 format. Default is True

Returns

cmapBQ.utils.long_to_gctx(df)

Converts long csv table to GCToo Object. Dataframe must have ‘rid’, ‘cid’ and ‘value’ columns No other columns or metadata is preserved.

Parameters

df – Long form pandas DataFrame

Returns

GCToo object

cmapBQ.utils.mk_out_dir(path, toolname, create_subdir=True)

cmapBQ.utils.parse_condition(arg, sep=',')

Parse argument for pathname, string or list. If file path exists reads GRP or TXT file. Non-path filenames are tokenized by specified delimiter, default is ‘,’. Returns list

Parameters

• arg – Takes in pathname, string, or list.

• sep – Delimiter to separate elements in string into list. Default is ‘,’

Returns

list

cmapBQ.utils.str2bool(v)

cmapBQ.utils.write_args(args, out_path)

cmapBQ.utils.write_status(success, out, exception='')