Merge pull request #272 from pachterlab/devel

Bump version: 0.29.0 → 0.29.1

Author: Yenaled

README.md

@@ -1,6 +1,6 @@
 # kb-python
-![github version](https://img.shields.io/badge/Version-0.29.0-informational)
-[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.28.0/)
+![github version](https://img.shields.io/badge/Version-0.29.1-informational)
+[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.29.1/)
 ![python versions](https://img.shields.io/pypi/pyversions/kb_python)
 ![status](https://github.com/pachterlab/kb_python/workflows/CI/badge.svg)
 [![codecov](https://codecov.io/gh/pachterlab/kb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/pachterlab/kb_python)
@@ -98,9 +98,9 @@ The `kb info` command prints out package information including the version of `k
 
 ```bash
 $ kb info
-kb_python 0.28.0 ...
-kallisto: 0.50.1 ...
-bustools: 0.43.1 ...
+kb_python 0.29.1 ...
+kallisto: 0.51.1 ...
+bustools: 0.44.1 ...
 ...
 ```
 ---

docs/conf.py

@@ -24,7 +24,7 @@
 author = 'Kyung Hoi (Joseph) Min'
 
 # The full version, including alpha/beta/rc tags
-release = '0.29.0'
+release = '0.29.1'
 master_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

docs/index.rst

@@ -6,7 +6,7 @@
 Welcome to kb-python's documentation!
 =====================================
 
-This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.29.0``.
+This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.29.1``.
 For user documentation and tutorials, please go to `kallisto | bustools <https://www.kallistobus.tools/>`_.
 
 Development Prerequisites

kb_python/__init__.py

@@ -1 +1 @@
-__version__ = '0.29.0'
+__version__ = '0.29.1'

kb_python/bins/darwin/bustools/bustools

@@ -263,7 +263,8 @@ def parse_ref(
             args.workflow,
             files,
             overwrite=args.overwrite,
-            temp_dir=temp_dir
+            temp_dir=temp_dir,
+            k=31 if not args.k else args.k
         )
     elif args.workflow == 'nac':
         ref_nac(
@@ -1846,9 +1847,8 @@ def main():
     logger.debug('Printing verbose output')
 
     # Set binary paths
-    if args.command in ('ref', 'count', 'extract') and ('dry_run' not in args
-                                                        or not args.dry_run):
-
+    if args.command in ('ref', 'count', 'extract'):
+        dry_run = not ('dry_run' not in args or not args.dry_run)
         use_kmer64 = False
         opt_off = False
         if args.k and args.k > 32:
@@ -1870,7 +1870,21 @@ def main():
         # Check
         kallisto_path = get_kallisto_binary_path()
         bustools_path = get_bustools_binary_path()
-        kallisto_ok, bustools_ok = test_binaries()
+        kallisto_ok = True
+        bustools_ok = True
+        if not dry_run:
+            kallisto_ok, bustools_ok = test_binaries()
+
+        # If kallisto binary is not OK, try one with opt-off if applicable
+        if not kallisto_ok and not opt_off and bustools_ok:
+            # Only do so if --kallisto not already provided
+            if not any(arg.startswith('--kallisto') for arg in sys.argv):
+                opt_off = True
+                set_special_kallisto_binary(use_kmer64, opt_off)
+                args.kallisto = get_provided_kallisto_path()
+                set_kallisto_binary_path(args.kallisto)
+                kallisto_path = get_kallisto_binary_path()
+                kallisto_ok, bustools_ok = test_binaries()
 
         if not kallisto_path or not kallisto_ok:
             raise UnsupportedOSError(
@@ -1885,8 +1899,9 @@ def main():
                 'run `kb compile`.'
             )
 
-        logger.debug(f'kallisto binary located at {kallisto_path}')
-        logger.debug(f'bustools binary located at {bustools_path}')
+        if not dry_run:
+            logger.debug(f'kallisto binary located at {kallisto_path}')
+            logger.debug(f'bustools binary located at {bustools_path}')
 
     temp_dir = args.tmp or (
         os.path.join(args.o, TEMP_DIR)

kb_python/bins/darwin/m1/bustools/bustools

@@ -383,7 +383,8 @@ def download_reference(
     workflow: str,
     files: Dict[str, str],
     temp_dir: str = 'tmp',
-    overwrite: bool = False
+    overwrite: bool = False,
+    k: int = 31
 ) -> Dict[str, str]:
     """Downloads a provided reference file from a static url.
 
@@ -395,6 +396,7 @@ def download_reference(
             paths to download the given reference have been provided
         temp_dir: Path to temporary directory, defaults to `tmp`
         overwrite: Overwrite an existing index file, defaults to `False`
+        k: k-mer size, defaults to `31` (only `31` and `63` are supported)
 
     Returns:
         Dictionary containing paths to generated file(s)
@@ -424,8 +426,15 @@ def download_reference(
                 f'The following workflow option is not supported: {workflow}'
             )
 
+        long = ""
+        if k == 63:
+            long = "_long"
+        elif k != 31:
+            logger.info(
+                "Only k-mer lengths 31 or 63 supported, defaulting to 31"
+            )
         url = "https://github.com/pachterlab/kallisto-transcriptome-indices/"
-        url = url + f'releases/download/v1/{species}_index_{workflow}.tar.xz'
+        url = url + f'releases/download/v1/{species}_index_{workflow}{long}.tar.xz'
         path = os.path.join(temp_dir, os.path.basename(url))
         logger.info(
             'Downloading files for {} ({} workflow) from {} to {}'.format(
@@ -627,7 +636,7 @@ def ref(
 
         if len(fasta_paths) > 1:
             raise RefError((
-                'Option `--a` does not support multiple FASTA files as input'
+                'Option `--aa` does not support multiple FASTA files as input'
                 'while no GTF file(s) provided'
             ))
         else:
@@ -668,6 +677,8 @@ def ref(
     if not glob.glob(f'{index_path}*') or overwrite:
         t2g_result = create_t2g_from_fasta(cdna_path, t2g_path, aa_flag=aa)
         results.update(t2g_result)
+        if index_path.upper() == "NONE":
+            return results
 
         if k and k != 31:
             logger.warning(
@@ -1009,6 +1020,8 @@ def ref_nac(
         )
         t2g_result = create_t2g_from_fasta(combined_path, t2g_path)
         results.update(t2g_result)
+        if index_path.upper() == "NONE":
+            return results
 
         if k and k != 31:
             logger.warning(