Source code for cmapPy.pandasGEXpress.subset


Extract a subset of data from a GCT(x) file using the command line. ids can
be provided as a list or as a path to a grp file. See subset_gctoo for the
equivalent method to be used on GCToo objects.

import logging
import sys
import os
import argparse

import cmapPy.pandasGEXpress.setup_GCToo_logger as setup_logger
import cmapPy.pandasGEXpress.parse_gct as parse_gct
import cmapPy.pandasGEXpress.parse_gctx as parse_gctx
import cmapPy.pandasGEXpress.subset_gctoo as sg
import cmapPy.pandasGEXpress.write_gct as wg
import cmapPy.pandasGEXpress.write_gct as wgx
import cmapPy.set_io.grp as grp

__author__ = "Lev Litichevskiy"
__email__ = ""

logger = logging.getLogger(setup_logger.LOGGER_NAME)

[docs]def build_parser(): """Build argument parser.""" parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter) # Required args parser.add_argument("--in_path", "-i", required=True, help="file path to input GCT(x) file") parser.add_argument("--rid", nargs="+", help="filepath to grp file or string array for including rows") parser.add_argument("--cid", nargs="+", help="filepath to grp file or string array for including cols") parser.add_argument("--exclude_rid", "-er", nargs="+", help="filepath to grp file or string array for excluding rows") parser.add_argument("--exclude_cid", "-ec", nargs="+", help="filepath to grp file or string array for excluding cols") parser.add_argument("--out_name", "-o", default="ds_subsetted.gct", help="what to name the output file") parser.add_argument("--out_type", default="gct", choices=["gct", "gctx"], help="whether to write output as GCT or GCTx") parser.add_argument("--verbose", "-v", action="store_true", default=False, help="whether to increase the # of messages reported")
return parser def main(): # Get args args = build_parser().parse_args(sys.argv[1:]) setup_logger.setup(verbose=args.verbose) subset_main(args)
[docs]def subset_main(args): """ Separate method from main() in order to make testing easier and to enable command-line access. """ # Read in each of the command line arguments rid = _read_arg(args.rid) cid = _read_arg(args.cid) exclude_rid = _read_arg(args.exclude_rid) exclude_cid = _read_arg(args.exclude_cid) # If GCT, use subset_gctoo if args.in_path.endswith(".gct"): in_gct = parse_gct.parse(args.in_path) out_gct = sg.subset_gctoo(in_gct, rid=rid, cid=cid, exclude_rid=exclude_rid, exclude_cid=exclude_cid) # If GCTx, use parse_gctx else: if (exclude_rid is not None) or (exclude_cid is not None): msg = "exclude_{rid,cid} args not currently supported for parse_gctx." raise(Exception(msg))"Using hyperslab selection functionality of parse_gctx...") out_gct = parse_gctx.parse(args.in_path, rid=rid, cid=cid) # Write the output gct if args.out_type == "gctx": wgx.write(out_gct, args.out_name) else:
wg.write(out_gct, args.out_name, data_null="NaN", metadata_null="NA", filler_null="NA") def _read_arg(arg): """ If arg is a list with 1 element that corresponds to a valid file path, use set_io.grp to read the grp file. Otherwise, check that arg is a list of strings. Args: arg (list or None) Returns: arg_out (list or None) """ # If arg is None, just return it back if arg is None: arg_out = arg else: # If len(arg) == 1 and arg[0] is a valid filepath, read it as a grp file if len(arg) == 1 and os.path.exists(arg[0]): arg_out =[0]) else: arg_out = arg # Make sure that arg_out is a list of strings assert isinstance(arg_out, list), "arg_out must be a list." assert type(arg_out[0]) == str, "arg_out must be a list of strings." return arg_out if __name__ == "__main__": main()