1 files changed, 0 insertions, 108 deletions
diff --git a/qc.py b/qc.py
deleted file mode 100644
index fee74cb..0000000
--- a/qc.py
+++ /dev/null
@@ -1,108 +0,0 @@
-"""Implements the command-line interface for the qc application"""
-import os
-import sys
-import argparse
-
-import magic
-
-from quality_control.errors import ParseError
-from quality_control.parsing import (
-    FileType,
-    parse_file,
-    strain_names,
-    parse_errors,
-    parse_strains)
-
-
-def is_file_mime(filepath, mimetype):
-    """Check that `filepath` has a mimetype of `mimetype` or `text/plain`"""
-    return magic.from_file(filepath, mime=True) in ("text/plain", mimetype)
-
-def cli_argument_parser():
-    """Create the parser for the CLI arguments"""
-    parser = argparse.ArgumentParser(
-        prog="qc", description = (
-            "Command-Line Interface program for quality control of data files"))
-    parser.add_argument(
-        "filetype",
-        help="The type of file to check",
-        choices=("average", "standard-error"))
-    parser.add_argument(
-        "filepath",
-        help=(
-            "The path to the file to be checked."
-            "If an absolute path is not provided, then the file will be relative to"
-            f"\t'{os.getcwd()}'"))
-    default_strains_file = os.path.join(
-        os.path.dirname(__file__), "strains.csv")
-    parser.add_argument(
-        "-s", "--strainsfile",
-        help=(
-            "Path to the file containing allowable strains/samples. "
-            f"[default '{default_strains_file}']"),
-        default=default_strains_file)
-
-    parser.add_argument(
-        "-v", "--verbose",
-        help="Controls whether to show extra output",
-        default=False, action="store_true")
-    return parser
-
-def check(filepath, filetype, strains, verbose=False):
-    """Check the file and print out results"""
-    try:
-        for line_num, line in enumerate(parse_file(
-                filepath, filetype, strains), start=1):
-            if verbose:
-                print(f"Checked line: {line_num}")
-
-        print(f"Successfully checked the file. No errors found.")
-    except ParseError as pe:
-        print("line\terrors")
-        for line_num, error in enumerate(
-                parse_errors(filepath, filetype, strains,
-                             pe.args[0]["line_number"]),
-                start = pe.args[0]["line_number"] + 1):
-            print(f"{line_num}\t{' '.join(error['message'])}")
-            
-
-def main():
-    """Entry point function"""
-    argparser = cli_argument_parser()
-    args = argparser.parse_args()
-    if not os.path.exists(args.filepath):
-        print("The file '{args.filepath}' does not exist.", file=sys.stderr)
-        return 1
-
-    if not os.path.exists(args.strainsfile):
-        print("The file '{args.strainsfile}' does not exist.", file=sys.stderr)
-        return 2
-
-    if not is_file_mime(args.filepath, "text/tab-separated-values"):
-        print(
-            f"The file '{args.filepath}' MUST be a tab-separated file.",
-            file=sys.stderr)
-        return 3
-
-    if not is_file_mime(args.strainsfile, "text/csv"):
-        print(
-            f"The file '{args.strainsfile}' MUST be a tab-separated file.",
-            file=sys.stderr)
-        return 4
-
-    if args.verbose:
-        print(f"Parsing the strain names from '{args.strainsfile}'")
-
-    strains = strain_names(parse_strains(os.path.realpath(args.strainsfile)))
-
-    filepath = os.path.realpath(args.filepath)
-    if args.verbose:
-        print(f"Checking '{filepath}' for errors")
-
-    check(
-        filepath, (
-            FileType.AVERAGE if args.filetype == "average"
-            else FileType.STANDARD_ERROR), strains)
-
-if __name__ == "__main__":
-    main()