fixing ncbi download commands

Author: Mike Lee

CHANGELOG.md

@@ -13,8 +13,14 @@
 
 -->
 
-## v1.13.10 (27-Feb-2026)
 
+## v1.13.11 (NOT RELEASED YET)
+
+### Changed
+- `bit-update-ncbi-taxonomy` replaced with `get-ncbi-tax-data` (prior still retained for now)
+
+
+## v1.13.10 (27-Feb-2026)
 
 ### Changed
 - `bit-get-cov-stats`
@@ -29,7 +35,6 @@
 - `bit-filter-seqs-by-length` renamed to `bit-filter-fasta-by-length` to be more specific (prior retained for now)
 
 
-
 ---
 
 ## v1.13.9 (25-Feb-2026)

bit/modules/dl_ncbi_assemblies.py

@@ -7,7 +7,7 @@
 from bit.modules.general import (color_text, check_files_are_found,
                                  attempt_to_make_dir, report_message)
 from bit.modules.ncbi.parse_assembly_summary import parse_assembly_summary
-from bit.modules.ncbi.get_ncbi_assembly_tables import get_ncbi_assembly_data
+from bit.modules.ncbi.get_ncbi_assembly_data import get_ncbi_assembly_data
 
 
 def dl_ncbi_assemblies(args):
@@ -32,7 +32,7 @@ def preflight_checks(args):
     if args.output_dir and not os.path.exists(args.output_dir):
         attempt_to_make_dir(args.output_dir)
 
-    get_ncbi_assembly_data()
+    get_ncbi_assembly_data(quiet=True)
 
 
 def setup(args):

…modules/ncbi/get_ncbi_assembly_tables.py …t/modules/ncbi/get_ncbi_assembly_data.pybit/modules/ncbi/get_ncbi_assembly_tables.py renamed to bit/modules/ncbi/get_ncbi_assembly_data.py bit/modules/ncbi/get_ncbi_assembly_tables.py renamed to bit/modules/ncbi/get_ncbi_assembly_data.py

@@ -9,7 +9,7 @@
 import os
 import argparse
 from datetime import date
-from bit.cli.common import CustomRichHelpFormatter
+from bit.cli.common import CustomRichHelpFormatter, add_help
 from bit.modules.general import (wprint, color_text,
                                  report_message, notify_premature_exit,
                                  download_with_tqdm)
@@ -23,14 +23,18 @@ def main():
     parser = argparse.ArgumentParser(
         description="This is a bit helper program to download NCBI assembly-summary tables.",
         epilog="Ex. usage: `get-ncbi-assembly-tables`",
-        formatter_class=CustomRichHelpFormatter
+        formatter_class=CustomRichHelpFormatter,
+        add_help=False
     )
 
+    parser.add_argument("-q", "--quiet", help="Exit silently if assembly data already present", action = "store_true")
     parser.add_argument("-f", "--force-update", help='Update the stored NCBI assembly tables', action = "store_true")
 
+    add_help(parser)
+
     args = parser.parse_args()
 
-    get_ncbi_assembly_data(force_update = args.force_update)
+    get_ncbi_assembly_data(force_update=args.force_update, quiet=args.quiet)
 
 ################################################################################
 
@@ -106,12 +110,17 @@ def download_ncbi_assembly_summary_data(location):
     with open(date_retrieved_path, "w") as outfile:
         outfile.write(date_retrieved + "\n")
 
-def get_ncbi_assembly_data(force_update=False):
+def get_ncbi_assembly_data(force_update=False, quiet=False):
 
     ncbi_dir = check_ncbi_assembly_info_location_var_is_set()
     data_present = check_if_data_present(ncbi_dir)
 
     if data_present and not force_update:
+        if not quiet:
+            report_message(f"Assembly data already present.")
+            report_message(f"Check it with `bit-data-locations`, or add `-f` to this program-call to force updating it.")
+            print()
+            return
         return
     else:
         download_ncbi_assembly_summary_data(ncbi_dir)

bit/modules/ncbi/get_ncbi_tax_data.py

@@ -9,7 +9,7 @@
 import os
 import argparse
 import tarfile
-from bit.cli.common import CustomRichHelpFormatter
+from bit.cli.common import CustomRichHelpFormatter, add_help
 from bit.modules.general import (wprint, color_text, report_message,
                                  notify_premature_exit, download_with_tqdm)
 
@@ -19,15 +19,19 @@ def main():
 
     parser = argparse.ArgumentParser(
         description="This is a bit helper program to download NCBI taxonomy data.",
-        epilog="Example usage: get-ncbi-tax-data",
-        formatter_class=CustomRichHelpFormatter
+        epilog="Example usage: `get-ncbi-tax-data`",
+        formatter_class=CustomRichHelpFormatter,
+        add_help=False
     )
 
+    parser.add_argument("-q", "--quiet", help="Exit silently if tax data already present", action = "store_true")
     parser.add_argument("-f", "--force-update", help='Update the stored NCBI taxonomy data', action = "store_true")
 
+    add_help(parser)
+
     args = parser.parse_args()
 
-    get_ncbi_tax_data(force_update=args.force_update)
+    get_ncbi_tax_data(force_update=args.force_update, quiet=args.quiet)
 
 ################################################################################
 
@@ -82,12 +86,17 @@ def download_ncbi_tax_data(location):
     os.remove(taxdump_path)
 
 
-def get_ncbi_tax_data(force_update=False):
+def get_ncbi_tax_data(force_update=False, quiet = False):
 
     ncbi_data_dir = check_tax_location_var_is_set()
     data_present = check_if_data_present(ncbi_data_dir)
 
     if data_present and not force_update:
+        if not quiet:
+            report_message(f"Tax data already present.")
+            report_message(f"Check it with `bit-data-locations`, or add `-f` to this program-call to force updating it.")
+            print()
+            return
         return
     else:
         download_ncbi_tax_data(ncbi_data_dir)

bit/scripts/bit-get-lineage-from-taxids

@@ -47,7 +47,7 @@ fi
 
 
 ### checking that ncbi tax data is present already, and downloading if it isn't
-helper-bit-get-ncbi-tax-data
+get-ncbi-tax-data --quiet
 
 if [ "${include_strain}" = true ]; then
     taxonkit_reformat_pattern='{domain|superkingdom}\t{phylum}\t{class}\t{order}\t{family}\t{genus}\t{species}\t{strain|subspecies|no rank}'

bit/scripts/bit-update-ncbi-taxonomy

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "bit"
-version = "1.13.10"
+version = "1.13.11"
 description = "A set of bioinformatics scripts and workflows"
 readme = "README.md"
 license = { text = "GPLv3" }
@@ -24,8 +24,9 @@ bit-version = "bit.modules.general:report_version"
 
 ## ncbi-related ##
 bit-dl-ncbi-assemblies = "bit.cli.dl_ncbi_assemblies:main"
-get-ncbi-assembly-tables = "bit.modules.ncbi.get_ncbi_assembly_tables:main"
+get-ncbi-assembly-data = "bit.modules.ncbi.get_ncbi_assembly_data:main"
 get-ncbi-tax-data = "bit.modules.ncbi.get_ncbi_tax_data:main"
+bit-update-ncbi-taxonomy = "bit.modules.ncbi.get_ncbi_tax_data:main"
 
 
 ## gtdb-related ##

bit/scripts/helper-bit-get-ncbi-tax-data

@@ -45,7 +45,7 @@ fi
 
 ## getting current version from setup.py (now pyproject.toml)
 # version=$(grep "version" setup.py | cut -f 2 -d '=' | tr -d '",')
-version=$(grep "version" pyproject.toml | cut -f 2 -d '=' | tr -d '" ')
+version=$(grep -w "^version" pyproject.toml | cut -f 2 -d '=' | tr -d '" ')
 ## getting current build from meta.yaml
 build=$(grep -A 1 ^build ${recipe_dir}/meta.yaml | grep number | cut -f 2 -d ":" | tr -s " " "\t" | cut -f 2)