mlbi-bitool 0.2.0__tar.gz → 0.2.2__tar.gz

{mlbi_bitool-0.2.0 → mlbi_bitool-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlbi-bitool
-Version: 0.2.0
+Version: 0.2.2
 Summary: Python interface to BioInfo tools for use in Google.Colab
 Author-email: MLBI Lab <syoon@dku.edu>
 License-Expression: MIT

{mlbi_bitool-0.2.0 → mlbi_bitool-0.2.2}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mlbi-bitool"
-version = "0.2.0"
+version = "0.2.2"
 description = "Python interface to BioInfo tools for use in Google.Colab"
 readme = "README.md"
 authors = [{ name = "MLBI Lab", email = "syoon@dku.edu" }]

{mlbi_bitool-0.2.0 → mlbi_bitool-0.2.2}/src/mlbi_bitool/bistack.py

@@ -140,6 +140,9 @@ def _print_status(name: str, version: Optional[str], installed_now: bool):
     vtxt = version or "unknown-version"
     print(f"{name}: {tag} (v{vtxt})")
 
+def _print_not_installed(name: str):
+    print(f"{name}: not installed")
+
 # -------------------- Java 버전 --------------------
 def _parse_java_version(text: str) -> Optional[Tuple[int,int,int,str]]:
     m = re.search(r'version\s+"(\d+)(?:\.(\d+))?(?:\.(\d+))?', text)
@@ -408,9 +411,13 @@ def _install_cnvkit(install: bool = True, pkg = 'cnvkit'):
 
 
 # -------------------- 메인 엔트리 --------------------
-def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False):
+def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False, install_local: bool = False):
     """
     Install/check common bioinformatics command-line tools.
+    In Google Colab, missing tools are installed by default.
+    In a local environment, installation is skipped by default and only tool
+    availability/version is reported. Pass install_local=True to allow local
+    installation attempts.
 
     Examples
     --------
@@ -420,13 +427,15 @@ def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False)
     >>> install_common_bi_tools("pacbio")
     >>> install_common_bi_tools("bi_training")
     >>> install_common_bi_tools(["bwa", "samtools", "gatk"], check_only=True)
+    >>> install_common_bi_tools("wes", install_local=True)
     """
 
     java_required_major = 17
     java_prefer = "conda"  # "apt" or "conda"
     java_allow_conda_fallback = True
 
-    check = check_only
+    is_colab = _is_colab()
+    allow_install = (not check_only) and (is_colab or install_local)
     lst_apt_pkgs = list(apt_pkgs.keys())
     lst_conda_pkgs = list(conda_pkgs.keys())
     lst_other_pkgs = list(other_pkgs.keys())
@@ -439,12 +448,15 @@ def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False)
     need_conda = bool(set(pkgs_to_install).intersection(lst_conda_pkgs))
     need_conda = need_conda or (java_prefer == "conda" and "gatk" in pkgs_to_install)
 
-    if need_conda and _is_colab():
-        ensure_condacolab(run_install=not check)
+    if not is_colab and not install_local:
+        print("Local environment detected. Installation is skipped; checking tool availability only.")
+
+    if need_conda and is_colab:
+        ensure_condacolab(run_install=allow_install)
 
     apt_cmd = "apt-get"
     need_apt = bool(set(pkgs_to_install).intersection(lst_apt_pkgs))
-    if need_apt and _which(apt_cmd) and _is_colab() and not check:
+    if need_apt and _which(apt_cmd) and is_colab and allow_install:
         _run(_sudo_prefix()+[apt_cmd, "update", "-y", "-qq"])
     elif need_apt and not _which(apt_cmd):
         print("%s not found; skipping APT tools." % apt_cmd)
@@ -452,15 +464,15 @@ def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False)
     for pkg in pkgs_to_install:
 
         if pkg in lst_apt_pkgs:
-            if _is_colab():
+            if is_colab or install_local:
                 arg = apt_pkgs[pkg]
-                _apt_ensure_and_report( arg, install =  not check, apt_cmd =apt_cmd )
+                _apt_ensure_and_report( arg, install=allow_install, apt_cmd=apt_cmd )
             else:
                 name, aptpkg, binname, vfunc = apt_pkgs[pkg]
                 if _which(binname):
                     _print_status(name, vfunc(), installed_now=False)
                 else:
-                    print("%s: not installed (APT install is only automatic in Colab)" % pkg)
+                    _print_not_installed(name)
 
         elif pkg in lst_conda_pkgs:
             spec = conda_pkgs[pkg]
@@ -470,8 +482,10 @@ def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False)
             if binpath:
                 v = vfunc()
                 _print_status(pkg, v, installed_now=False)
-            elif not check:
-                _conda_install(package = conda_pkg, install = not check, ensure_channels = True)
+            elif allow_install:
+                _conda_install(package=conda_pkg, install=True, ensure_channels=True)
+            else:
+                _print_not_installed(pkg)
 
         elif pkg == 'gatk':
             binname, vfunc = other_pkgs[pkg]
@@ -479,7 +493,7 @@ def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False)
             if binpath:
                 v = vfunc()
                 _print_status(pkg, v, installed_now=False)
-            elif not check:
+            elif allow_install:
                 # install Java
                 jv = _get_java_version()
                 if jv and jv[0] >= java_required_major:
@@ -488,7 +502,9 @@ def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False)
                     v2 = _ensure_java(java_required_major, prefer=java_prefer, allow_conda_fallback=java_allow_conda_fallback)
                     _print_status(f"Java (requires ≥{java_required_major})", v2, installed_now=True)
 
-                _install_gatk(install = not check)
+                _install_gatk(install=True)
+            else:
+                _print_not_installed(pkg)
 
         elif pkg == 'cnvkit':
             binname, vfunc = other_pkgs[pkg]
@@ -496,8 +512,10 @@ def install_common_bi_tools(pkgs_to_install: List[str] = None, check_only=False)
             if binpath:
                 v = vfunc()
                 _print_status(pkg, v, installed_now=False)
-            elif not check:
-                _install_cnvkit(install = not check)
+            elif allow_install:
+                _install_cnvkit(install=True)
+            else:
+                _print_not_installed(pkg)
 
         else:
             print("%s: not supported" % pkg)

{mlbi_bitool-0.2.0 → mlbi_bitool-0.2.2}/src/mlbi_bitool/load_datasets.py

@@ -385,34 +385,26 @@ def decompress_tar_gz_folder(file_in, remove_org=True):
 
 
 bi_sample_data_fid_dict = {
-    'BI_RefGenome_hg38_sel':          '1uIHwlS3N4TsN7sJdD3j5Hf8B_clTQXHl',
-    'BI_Files_for_GATK':              '1pbMIMvoqBqGE9yMKUg2E-f2m4P8mmN4Y',
-    'BI_Files_for_GATK_full':         '13qwSu1e7d7olhKmpEuZYLSNShNCXfLkH',
-    'BI_WES_PDAC_chr17':              '1l88p48edaw7oHTSdCFQgXALoUAdYr2nT',
-    'BI_WES_PDAC_chr17_bam':          '1xCiTuVPqLytx5NTxmaIQcLXoUGPP-XZ7',
-    'BI_RNAseq_pacbio_chr12':         '13X-UBFJYlwgJXS-m5Bz5tqoe97TZFqZD',
-    'BI_RNAseq_pacbio_chr12_bam':     '1yDmQDjkkoHh9WP28PRp_vOr1r9YJMPmp',
-    'RefGenome_hg38_sel':             '1uIHwlS3N4TsN7sJdD3j5Hf8B_clTQXHl',
-    'Files_for_GATK_chr12':           '1pbMIMvoqBqGE9yMKUg2E-f2m4P8mmN4Y',  
-    'Files_for_GATK':                 '13qwSu1e7d7olhKmpEuZYLSNShNCXfLkH',    
-    'WES_PDAC_chr12': 		          '1l88p48edaw7oHTSdCFQgXALoUAdYr2nT',
-    'WES_PDAC_chr12_bam': 	          '1xCiTuVPqLytx5NTxmaIQcLXoUGPP-XZ7',
-    'WES_PDAC_chr12_SNV_CNV_results': '1V1tQQaMinXQvnjYT5y8FkqjDLksRY7-X',
-    'WES_NSCLC_chr7': 	              '1OIWarGf6Q9SN9sUjtvH1jqjm4apj5q28', 
-    'WES_NSCLC_chr7_bam': 	          '1uSJ0l9bKhX3E90WLRs9QRwyHo1Ljtsmp', 
-    'RNAseq_PDAC_chr12':              '1RAVk6NxIyl-lyrwh0qoNu0Vm4R2V5ht9', 
-    'RNAseq_PDAC_chr12_bam':          '1g0kBnw0s-6AuGieuW-O1-4pSsftk0sn9', 
-    'RNAseq_NSCLC_chr7':              '1HF9N5USGkhxpjzsLmChAqtiIP4OuwelM', 
-    'RNAseq_NSCLC_chr7_bam':          '1Ek2gTTGPPcaXqVee4XThcx7BgDgv9_5w', 
-    'RNAseq_CRC_chr17': 	          '1KbV3o6r4pVPtlQur0xyiniJYS01DsPpM', 
-    'RNAseq_CRC_chr17_bam':           '13FOOKwlMFgKJCg5-5x5gft0--zzHWAUc', 
-    'RNAseq_CRC_chr17_gexp_results':  '1kJLU5AGuX4XmC1AbhX1kkn6F3A3jWtYD',
-    'RNAseq_pacbio_chr7':             '1vIpKKmwpKz4XyRhCsUQ_CMQZrVOPNigZ',
-    # 'RNAseq_pacbio_chr7_bam': '',
-    'index_bwa_hg38_sel':             '1Ed9aMgOCmoFKYKj6-3WbEmQqepzRKUqJ',
-    'index_star_hg38_sel':            '1VnU8oqEUPMViNX0QybywbW2jPY0Z1u4a',
-    'index_rsem_hg38_sel':            '1Sy3DFcacd3sM3Fqi1egJhVfG4ZTWqD9i',
-    'index_salmon_hg38_sel':          '1Q9yhzWuMdgHcNVUdNQGBjvTG307tzoD9',
+    'BI_RefGenome_hg38_sel':             '1uIHwlS3N4TsN7sJdD3j5Hf8B_clTQXHl',
+    'BI_Files_for_GATK_chr12':           '1pbMIMvoqBqGE9yMKUg2E-f2m4P8mmN4Y',  
+    'BI_Files_for_GATK':                 '13qwSu1e7d7olhKmpEuZYLSNShNCXfLkH',    
+    'BI_WES_PDAC_chr12': 		         '1l88p48edaw7oHTSdCFQgXALoUAdYr2nT',
+    'BI_WES_PDAC_chr12_bam': 	         '1xCiTuVPqLytx5NTxmaIQcLXoUGPP-XZ7',
+    'BI_WES_PDAC_chr12_SNV_CNV_results': '1V1tQQaMinXQvnjYT5y8FkqjDLksRY7-X',
+    'BI_WES_NSCLC_chr7': 	             '1OIWarGf6Q9SN9sUjtvH1jqjm4apj5q28', 
+    'BI_WES_NSCLC_chr7_bam': 	         '1uSJ0l9bKhX3E90WLRs9QRwyHo1Ljtsmp', 
+    'BI_RNAseq_PDAC_chr12':              '1RAVk6NxIyl-lyrwh0qoNu0Vm4R2V5ht9', 
+    'BI_RNAseq_PDAC_chr12_bam':          '1g0kBnw0s-6AuGieuW-O1-4pSsftk0sn9', 
+    'BI_RNAseq_NSCLC_chr7':              '1HF9N5USGkhxpjzsLmChAqtiIP4OuwelM', 
+    'BI_RNAseq_NSCLC_chr7_bam':          '1Ek2gTTGPPcaXqVee4XThcx7BgDgv9_5w', 
+    'BI_RNAseq_CRC_chr17': 	             '1KbV3o6r4pVPtlQur0xyiniJYS01DsPpM', 
+    'BI_RNAseq_CRC_chr17_bam':           '13FOOKwlMFgKJCg5-5x5gft0--zzHWAUc', 
+    'BI_RNAseq_CRC_chr17_gexp_results':  '1kJLU5AGuX4XmC1AbhX1kkn6F3A3jWtYD',
+    'BI_RNAseq_pacbio_chr7':             '1vIpKKmwpKz4XyRhCsUQ_CMQZrVOPNigZ',
+    'BI_index_bwa_hg38_sel':             '1Ed9aMgOCmoFKYKj6-3WbEmQqepzRKUqJ',
+    'BI_index_star_hg38_sel':            '1VnU8oqEUPMViNX0QybywbW2jPY0Z1u4a',
+    'BI_index_rsem_hg38_sel':            '1Sy3DFcacd3sM3Fqi1egJhVfG4ZTWqD9i',
+    'BI_index_salmon_hg38_sel':          '1Q9yhzWuMdgHcNVUdNQGBjvTG307tzoD9',
     'ML_TCGA_BRCA':                   '1YHJwzdDwQx0KDhmn2fndB9j5leBBx8hH',
     'ML_METABRIC':                    '1b3cPWwz_CG86s4TGnfCjxCP7KVh2UPHR',
     'ML_CCLE_CTRPv2':                 '1q2XqSycVSrgFPJ4FUI2qWHxIKqYYTdij',            

{mlbi_bitool-0.2.0 → mlbi_bitool-0.2.2}/src/mlbi_bitool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mlbi-bitool
-Version: 0.2.0
+Version: 0.2.2
 Summary: Python interface to BioInfo tools for use in Google.Colab
 Author-email: MLBI Lab <syoon@dku.edu>
 License-Expression: MIT