- adding bit-get-test-data program

- removed the deprecated bit-median-ratio-norm, as that is encompassed in bit-normalize-table
- removed the stub-bit-GTDB-tax-to-NCBI-tax as that type of path is no longer needed, it is probably better to do a different quick taxonomy assignment method to NCBI, like with sourmash or other

bit/bit-get-test-data

@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+
+"""
+This is a program for downloading test data files. 
+"""
+
+import sys
+import os
+import argparse
+import textwrap
+
+parser = argparse.ArgumentParser(description = "This is a helper program for downloading test data for use with bit workflows and programs. For bit verison info run `bit-version`. ",
+                                 epilog="Ex. usage: bit-get-test-data metagenomics\n")
+
+required = parser.add_argument_group('required arguments')
+
+required.add_argument('datatype', choices = ['metagenomics'],
+                                           help = "The first positional argument should be what type of test data you'd like to download")
+
+if len(sys.argv)==1:
+    parser.print_help(sys.stderr)
+    sys.exit(0)
+
+args = parser.parse_args()
+
+
+################################################################################
+
+def main():
+
+    dl_test_data()
+
+################################################################################
+
+### variables and functions ###
+
+tty_colors = {
+    'green' : '\033[0;32m%s\033[0m',
+    'yellow' : '\033[0;33m%s\033[0m',
+    'red' : '\033[0;31m%s\033[0m'
+}
+
+def color_text(text, color='green'):
+    if sys.stdout.isatty():
+        return tty_colors[color] % text
+    else:
+        return text
+
+
+def wprint(text):
+    print(textwrap.fill(text, width=80, initial_indent="  ", 
+          subsequent_indent="  ", break_on_hyphens=False))
+
+
+def report_message(message, color = "yellow"):
+    print("")
+    wprint(color_text(message, color))
+
+
+def dl_test_data():
+
+    """ main function for downloading test data """
+
+    if args.datatype == "metagenomics":
+
+        report_message("Downloading and unpacking 2 paired-end Illumina metagenomics test samples (4 files, ~800 MB total; they are kinda large for test data so MAGs can be recovered):")
+        print("")
+
+        # getting the metagenomics test data
+        os.system("curl -L -o test-metagenomics-reads.zip https://figshare.com/ndownloader/files/46096083")
+
+        # extracting
+        os.system("unzip -qo test-metagenomics-reads.zip")
+
+        # removing archive
+        os.system("rm test-metagenomics-reads.zip")
+
+        report_message("Pulled metagenomics (Illumina) reads for two test samples from here:", "green")
+        print("    https://figshare.com/account/projects/203736/articles/25750935\n")
+
+    else:
+
+        report_message("The data type you requested is not currently available.", "red")
+
+        print("\n    Please check the currently available data types with 'bit-get-test-data --help'\n")
+
+
+################################################################################
+
+if __name__ == "__main__":
+    main()

bit/bit-version

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-version='1.9.0'
+version='1.9.1'
 
 GREEN='\033[0;32m'
 NC='\033[0m'