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'/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/__init__.py', + 'PYMODULE'), + ('xml.parsers', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/parsers/__init__.py', + 'PYMODULE'), + ('xml.parsers.expat', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/parsers/expat.py', + 'PYMODULE'), + ('xml.sax', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/sax/__init__.py', + 'PYMODULE'), + ('xml.sax._exceptions', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/sax/_exceptions.py', + 'PYMODULE'), + ('xml.sax.expatreader', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/sax/expatreader.py', + 'PYMODULE'), + ('xml.sax.handler', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/sax/handler.py', + 'PYMODULE'), + ('xml.sax.saxutils', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/sax/saxutils.py', + 'PYMODULE'), + ('xml.sax.xmlreader', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xml/sax/xmlreader.py', + 'PYMODULE'), + ('xmlrpc', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xmlrpc/__init__.py', + 'PYMODULE'), + ('xmlrpc.client', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/xmlrpc/client.py', + 'PYMODULE'), + ('zipfile', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/zipfile.py', + 'PYMODULE'), + ('zipimport', + '/sw/pkgs/arc/python/3.10.4/lib/python3.10/zipimport.py', + 'PYMODULE')]) diff --git a/build/snpkit/base_library.zip b/build/snpkit/base_library.zip new file mode 100644 index 0000000..28aee5a Binary files /dev/null and b/build/snpkit/base_library.zip differ diff --git a/build/snpkit/snpkit.pkg b/build/snpkit/snpkit.pkg new file mode 100644 index 0000000..3844dfd Binary files /dev/null and b/build/snpkit/snpkit.pkg differ diff --git a/build/snpkit/warn-snpkit.txt b/build/snpkit/warn-snpkit.txt new file mode 100644 index 0000000..839fde6 --- /dev/null +++ b/build/snpkit/warn-snpkit.txt @@ -0,0 +1,35 @@ + +This file lists modules PyInstaller was not able to find. This does not +necessarily mean this module is required for running your program. Python and +Python 3rd-party packages include a lot of conditional or optional modules. For +example the module 'ntpath' only exists on Windows, whereas the module +'posixpath' only exists on Posix systems. + +Types if import: +* top-level: imported at the top-level - look at these first +* conditional: imported within an if-statement +* delayed: imported within a function +* optional: imported within a try-except-statement + +IMPORTANT: Do NOT post this list to the issue-tracker. Use it as a basis for + tracking down the missing module yourself. Thanks! + +missing module named pyimod02_importers - imported by /home/apirani/.local/lib/python3.10/site-packages/PyInstaller/hooks/rthooks/pyi_rth_pkgutil.py (top-level) +missing module named pep517 - imported by importlib.metadata (delayed) +missing module named 'org.python' - imported by copy (optional), xml.sax (delayed, conditional) +missing module named org - imported by pickle (optional) +missing module named winreg - imported by importlib._bootstrap_external (conditional), mimetypes (optional), urllib.request (delayed, conditional, optional) +missing module named nt - imported by os (delayed, conditional, optional), ntpath (optional), shutil (conditional), importlib._bootstrap_external (conditional), ctypes (delayed, conditional) +excluded module named _frozen_importlib - imported by importlib (optional), importlib.abc (optional), zipimport (top-level) +missing module named _frozen_importlib_external - imported by importlib._bootstrap (delayed), importlib (optional), importlib.abc (optional), zipimport (top-level) +missing module named java - imported by xml.sax._exceptions (conditional) +missing module named _winapi - imported by encodings (delayed, conditional, optional), subprocess (optional), mimetypes (optional), multiprocessing.connection (optional), multiprocessing.spawn (delayed, conditional), multiprocessing.reduction (conditional), multiprocessing.shared_memory (conditional), multiprocessing.heap (conditional), multiprocessing.popen_spawn_win32 (top-level) +missing module named multiprocessing.BufferTooShort - imported by multiprocessing (top-level), multiprocessing.connection (top-level) +missing module named multiprocessing.AuthenticationError - imported by multiprocessing (top-level), multiprocessing.connection (top-level) +missing module named multiprocessing.get_context - imported by multiprocessing (top-level), multiprocessing.pool (top-level), multiprocessing.managers (top-level), multiprocessing.sharedctypes (top-level) +missing module named multiprocessing.TimeoutError - imported by multiprocessing (top-level), multiprocessing.pool (top-level) +missing module named msvcrt - imported by subprocess (optional), getpass (optional), multiprocessing.spawn (delayed, conditional), multiprocessing.popen_spawn_win32 (top-level) +missing module named multiprocessing.set_start_method - imported by multiprocessing (top-level), multiprocessing.spawn (top-level) +missing module named multiprocessing.get_start_method - imported by multiprocessing (top-level), multiprocessing.spawn (top-level) +missing module named _scproxy - imported by urllib.request (conditional) +missing module named subprocess32 - imported by modules.logging_subprocess (conditional), logging_subprocess (conditional) diff --git a/build/snpkit/xref-snpkit.html b/build/snpkit/xref-snpkit.html new file mode 100644 index 0000000..eb43e89 --- /dev/null +++ b/build/snpkit/xref-snpkit.html @@ -0,0 +1,9335 @@ + + + + + modulegraph cross reference for pyi_rth_inspect.py, pyi_rth_multiprocessing.py, pyi_rth_pkgutil.py, snpkit.py + + + +

modulegraph cross reference for pyi_rth_inspect.py, pyi_rth_multiprocessing.py, pyi_rth_pkgutil.py, snpkit.py

+ +
+ + pyi_rth_inspect.py +Script
+imports: + inspect + • os + • sys + +
+
+imported by: + snpkit.py + +
+ +
+ +
+ + pyi_rth_multiprocessing.py +Script
+imports: + multiprocessing + • multiprocessing.popen_fork + • multiprocessing.popen_spawn_posix + • multiprocessing.popen_spawn_win32 + • multiprocessing.spawn + • os + • subprocess + • sys + • threading + +
+
+imported by: + snpkit.py + +
+ +
+ +
+ + pyi_rth_pkgutil.py +Script
+imports: + os + • pkgutil + • pyimod02_importers + • sys + +
+
+imported by: + snpkit.py + +
+ +
+ +
+ + snpkit.py +Script
+imports: + _collections_abc + • _weakrefset + • abc + • argparse + • codecs + • collections + • collections.abc + • config_settings + • configparser + • copyreg + • datetime + • encodings + • encodings.aliases + • encodings.ascii + • encodings.base64_codec + • encodings.big5 + • encodings.big5hkscs + • encodings.bz2_codec + • encodings.charmap + • encodings.cp037 + • encodings.cp1006 + • encodings.cp1026 + • encodings.cp1125 + • encodings.cp1140 + • encodings.cp1250 + • encodings.cp1251 + • encodings.cp1252 + • encodings.cp1253 + • encodings.cp1254 + • encodings.cp1255 + • encodings.cp1256 + • encodings.cp1257 + • encodings.cp1258 + • encodings.cp273 + • encodings.cp424 + • encodings.cp437 + • encodings.cp500 + • encodings.cp720 + • encodings.cp737 + • encodings.cp775 + • encodings.cp850 + • encodings.cp852 + • encodings.cp855 + • encodings.cp856 + • encodings.cp857 + • encodings.cp858 + • encodings.cp860 + • encodings.cp861 + • encodings.cp862 + • encodings.cp863 + • encodings.cp864 + • encodings.cp865 + • encodings.cp866 + • encodings.cp869 + • encodings.cp874 + • encodings.cp875 + • encodings.cp932 + • encodings.cp949 + • encodings.cp950 + • encodings.euc_jis_2004 + • encodings.euc_jisx0213 + • encodings.euc_jp + • encodings.euc_kr + • encodings.gb18030 + • encodings.gb2312 + • encodings.gbk + • encodings.hex_codec + • encodings.hp_roman8 + • encodings.hz + • encodings.idna + • encodings.iso2022_jp + • encodings.iso2022_jp_1 + • encodings.iso2022_jp_2 + • encodings.iso2022_jp_2004 + • encodings.iso2022_jp_3 + • encodings.iso2022_jp_ext + • encodings.iso2022_kr + • encodings.iso8859_1 + • encodings.iso8859_10 + • encodings.iso8859_11 + • encodings.iso8859_13 + • encodings.iso8859_14 + • encodings.iso8859_15 + • encodings.iso8859_16 + • encodings.iso8859_2 + • encodings.iso8859_3 + • encodings.iso8859_4 + • encodings.iso8859_5 + • encodings.iso8859_6 + • encodings.iso8859_7 + • encodings.iso8859_8 + • encodings.iso8859_9 + • encodings.johab + • encodings.koi8_r + • encodings.koi8_t + • encodings.koi8_u + • encodings.kz1048 + • encodings.latin_1 + • encodings.mac_arabic + • encodings.mac_croatian + • encodings.mac_cyrillic + • encodings.mac_farsi + • encodings.mac_greek + • encodings.mac_iceland + • encodings.mac_latin2 + • encodings.mac_roman + • encodings.mac_romanian + • encodings.mac_turkish + • encodings.mbcs + • encodings.oem + • encodings.palmos + • encodings.ptcp154 + • encodings.punycode + • encodings.quopri_codec + • encodings.raw_unicode_escape + • encodings.rot_13 + • encodings.shift_jis + • encodings.shift_jis_2004 + • encodings.shift_jisx0213 + • encodings.tis_620 + • encodings.undefined + • encodings.unicode_escape + • encodings.utf_16 + • encodings.utf_16_be + • encodings.utf_16_le + • encodings.utf_32 + • encodings.utf_32_be + • encodings.utf_32_le + • encodings.utf_7 + • encodings.utf_8 + • encodings.utf_8_sig + • encodings.uu_codec + • encodings.zlib_codec + • enum + • errno + • fnmatch + • functools + • genericpath + • glob + • heapq + • io + • keyword + • linecache + • locale + • modules.log_modules + • modules.logging_subprocess + • modules.phage_detection + • modules.snpeff + • modules.variant_diagnostics.find_repeats + • modules.variant_diagnostics.mask_regions + • multiprocessing + • ntpath + • operator + • os + • pathlib + • posixpath + • pyi_rth_inspect.py + • pyi_rth_multiprocessing.py + • pyi_rth_pkgutil.py + • re + • reprlib + • shutil + • sre_compile + • sre_constants + • sre_parse + • stat + • subprocess + • sys + • token + • tokenize + • traceback + • types + • urllib + • urllib.error + • urllib.parse + • urllib.request + • urllib.response + • urllib.robotparser + • warnings + • weakref + +
+ +
+ +
+ + 'org.python' +MissingModule
+imported by: + copy + • xml.sax + +
+ +
+ +
+ + _abc (builtin module)
+imported by: + abc + +
+ +
+ +
+ + _ast (builtin module)
+imported by: + ast + +
+ +
+ +
+ + _bisect /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_bisect.cpython-310-x86_64-linux-gnu.so
+imported by: + bisect + +
+ +
+ +
+ + _blake2 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_blake2.cpython-310-x86_64-linux-gnu.so
+imported by: + hashlib + +
+ +
+ +
+ + _bz2 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_bz2.cpython-310-x86_64-linux-gnu.so
+imported by: + bz2 + +
+ +
+ +
+ + _codecs (builtin module)
+imported by: + codecs + +
+ +
+ +
+ + _codecs_cn /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_codecs_cn.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.gb18030 + • encodings.gb2312 + • encodings.gbk + • encodings.hz + +
+ +
+ +
+ + _codecs_hk /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_codecs_hk.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.big5hkscs + +
+ +
+ +
+ + _codecs_iso2022 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_codecs_iso2022.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.iso2022_jp + • encodings.iso2022_jp_1 + • encodings.iso2022_jp_2 + • encodings.iso2022_jp_2004 + • encodings.iso2022_jp_3 + • encodings.iso2022_jp_ext + • encodings.iso2022_kr + +
+ +
+ +
+ + _codecs_jp /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_codecs_jp.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.cp932 + • encodings.euc_jis_2004 + • encodings.euc_jisx0213 + • encodings.euc_jp + • encodings.shift_jis + • encodings.shift_jis_2004 + • encodings.shift_jisx0213 + +
+ +
+ +
+ + _codecs_kr /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_codecs_kr.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.cp949 + • encodings.euc_kr + • encodings.johab + +
+ +
+ +
+ + _codecs_tw /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_codecs_tw.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.big5 + • encodings.cp950 + +
+ +
+ +
+ + _collections (builtin module)
+imported by: + collections + • threading + +
+ +
+ +
+ + _collections_abc +SourceModule
+imports: + abc + • sys + +
+
+imported by: + collections + • collections.abc + • contextlib + • locale + • os + • pathlib + • random + • snpkit.py + • types + • weakref + +
+ +
+ +
+ + _compat_pickle +SourceModule
+imported by: + _pickle + • pickle + +
+ +
+ +
+ + _compression +SourceModule
+imports: + io + • sys + +
+
+imported by: + bz2 + • gzip + • lzma + +
+ +
+ +
+ + _contextvars /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_contextvars.cpython-310-x86_64-linux-gnu.so
+imported by: + contextvars + +
+ +
+ +
+ + _csv /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_csv.cpython-310-x86_64-linux-gnu.so
+imported by: + csv + +
+ +
+ +
+ + _ctypes /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_ctypes.cpython-310-x86_64-linux-gnu.so
+imported by: + ctypes + +
+ +
+ +
+ + _datetime /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_datetime.cpython-310-x86_64-linux-gnu.so
+imports: + _strptime + • time + +
+
+imported by: + datetime + +
+ +
+ +
+ + _decimal /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_decimal.cpython-310-x86_64-linux-gnu.so
+imported by: + decimal + +
+ +
+ +
+ + _frozen_importlib +ExcludedModule
+imported by: + importlib + • importlib.abc + • zipimport + +
+ +
+ +
+ + _frozen_importlib_external +MissingModule
+imported by: + importlib + • importlib._bootstrap + • importlib.abc + • zipimport + +
+ +
+ +
+ + _functools (builtin module)
+imported by: + functools + +
+ +
+ +
+ + _hashlib /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_hashlib.cpython-310-x86_64-linux-gnu.so
+imported by: + hashlib + • hmac + +
+ +
+ +
+ + _heapq /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_heapq.cpython-310-x86_64-linux-gnu.so
+imported by: + heapq + +
+ +
+ +
+ + _imp (builtin module)
+imported by: + importlib + • importlib._bootstrap_external + • importlib.util + • zipimport + +
+ +
+ +
+ + _io (builtin module)
+imported by: + importlib._bootstrap_external + • io + • zipimport + +
+ +
+ +
+ + _json /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_json.cpython-310-x86_64-linux-gnu.so
+imports: + json.decoder + +
+
+imported by: + json.decoder + • json.encoder + • json.scanner + +
+ +
+ +
+ + _locale (builtin module)
+imported by: + locale + • re + +
+ +
+ +
+ + _lzma /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_lzma.cpython-310-x86_64-linux-gnu.so
+imported by: + lzma + +
+ +
+ +
+ + _md5 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_md5.cpython-310-x86_64-linux-gnu.so
+imported by: + hashlib + +
+ +
+ +
+ + _multibytecodec /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_multibytecodec.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.big5 + • encodings.big5hkscs + • encodings.cp932 + • encodings.cp949 + • encodings.cp950 + • encodings.euc_jis_2004 + • encodings.euc_jisx0213 + • encodings.euc_jp + • encodings.euc_kr + • encodings.gb18030 + • encodings.gb2312 + • encodings.gbk + • encodings.hz + • encodings.iso2022_jp + • encodings.iso2022_jp_1 + • encodings.iso2022_jp_2 + • encodings.iso2022_jp_2004 + • encodings.iso2022_jp_3 + • encodings.iso2022_jp_ext + • encodings.iso2022_kr + • encodings.johab + • encodings.shift_jis + • encodings.shift_jis_2004 + • encodings.shift_jisx0213 + +
+ +
+ +
+ + _multiprocessing /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_multiprocessing.cpython-310-x86_64-linux-gnu.so
+imported by: + multiprocessing.connection + • multiprocessing.queues + • multiprocessing.resource_tracker + • multiprocessing.synchronize + +
+ +
+ +
+ + _opcode /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_opcode.cpython-310-x86_64-linux-gnu.so
+imported by: + opcode + +
+ +
+ +
+ + _operator (builtin module)
+imported by: + hmac + • operator + +
+ +
+ +
+ + _pickle /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_pickle.cpython-310-x86_64-linux-gnu.so
+imports: + _compat_pickle + • codecs + • copyreg + +
+
+imported by: + pickle + +
+ +
+ +
+ + _posixshmem /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_posixshmem.cpython-310-x86_64-linux-gnu.so
+imported by: + multiprocessing.resource_tracker + • multiprocessing.shared_memory + +
+ +
+ +
+ + _posixsubprocess /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_posixsubprocess.cpython-310-x86_64-linux-gnu.so
+imports: + gc + +
+
+imported by: + multiprocessing.util + • subprocess + +
+ +
+ +
+ + _py_abc +SourceModule
+imports: + _weakrefset + +
+
+imported by: + abc + +
+ +
+ +
+ + _pydecimal +SourceModule
+imports: + collections + • contextvars + • itertools + • locale + • math + • numbers + • re + • sys + +
+
+imported by: + decimal + +
+ +
+ +
+ + _queue /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_queue.cpython-310-x86_64-linux-gnu.so
+imported by: + queue + +
+ +
+ +
+ + _random /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_random.cpython-310-x86_64-linux-gnu.so
+imported by: + random + +
+ +
+ +
+ + _scproxy +MissingModule
+imported by: + urllib.request + +
+ +
+ +
+ + _sha1 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_sha1.cpython-310-x86_64-linux-gnu.so
+imported by: + hashlib + +
+ +
+ +
+ + _sha256 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_sha256.cpython-310-x86_64-linux-gnu.so
+imported by: + hashlib + +
+ +
+ +
+ + _sha3 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_sha3.cpython-310-x86_64-linux-gnu.so
+imported by: + hashlib + +
+ +
+ +
+ + _sha512 /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_sha512.cpython-310-x86_64-linux-gnu.so
+imported by: + hashlib + • random + +
+ +
+ +
+ + _signal (builtin module)
+imported by: + signal + +
+ +
+ +
+ + _socket /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_socket.cpython-310-x86_64-linux-gnu.so
+imported by: + socket + +
+ +
+ +
+ + _sre (builtin module)
+imports: + copy + • re + +
+
+imported by: + sre_compile + • sre_constants + +
+ +
+ +
+ + _ssl /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_ssl.cpython-310-x86_64-linux-gnu.so
+imports: + socket + +
+
+imported by: + ssl + +
+ +
+ +
+ + _stat (builtin module)
+imported by: + stat + +
+ +
+ +
+ + _statistics /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_statistics.cpython-310-x86_64-linux-gnu.so
+imported by: + statistics + +
+ +
+ +
+ + _string (builtin module)
+imported by: + string + +
+ +
+ +
+ + _strptime +SourceModule
+imports: + _thread + • calendar + • datetime + • locale + • re + • time + +
+
+imported by: + _datetime + • datetime + • time + +
+ +
+ +
+ + _struct /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/_struct.cpython-310-x86_64-linux-gnu.so
+imported by: + struct + +
+ +
+ +
+ + _thread (builtin module)
+imported by: + _strptime + • dataclasses + • functools + • reprlib + • tempfile + • threading + +
+ +
+ +
+ + _threading_local +SourceModule
+imports: + contextlib + • threading + • weakref + +
+
+imported by: + threading + +
+ +
+ +
+ + _tracemalloc (builtin module)
+imported by: + tracemalloc + +
+ +
+ +
+ + _warnings (builtin module)
+imported by: + importlib._bootstrap_external + • warnings + • zipimport + +
+ +
+ +
+ + _weakref (builtin module)
+imported by: + _weakrefset + • collections + • weakref + • xml.sax.expatreader + +
+ +
+ +
+ + _weakrefset +SourceModule
+imports: + _weakref + • types + +
+
+imported by: + _py_abc + • multiprocessing.process + • snpkit.py + • threading + • weakref + +
+ +
+ +
+ + _winapi +MissingModule
+imported by: + encodings + • mimetypes + • multiprocessing.connection + • multiprocessing.heap + • multiprocessing.popen_spawn_win32 + • multiprocessing.reduction + • multiprocessing.shared_memory + • multiprocessing.spawn + • subprocess + +
+ +
+ +
+ + abc +SourceModule
+imports: + _abc + • _py_abc + +
+
+imported by: + _collections_abc + • contextlib + • dataclasses + • email._policybase + • functools + • importlib._abc + • importlib.abc + • importlib.metadata + • inspect + • io + • multiprocessing.reduction + • numbers + • os + • selectors + • snpkit.py + • typing + +
+ +
+ +
+ + argparse +SourceModule
+imports: + copy + • gettext + • os + • re + • shutil + • sys + • textwrap + • warnings + +
+
+imported by: + ast + • calendar + • dis + • gzip + • inspect + • py_compile + • snpkit.py + • tarfile + • tokenize + • zipfile + +
+ +
+ +
+ + array /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/array.cpython-310-x86_64-linux-gnu.so
+imported by: + multiprocessing.dummy + • multiprocessing.managers + • multiprocessing.reduction + • socket + +
+ +
+ +
+ + ast +SourceModule
+imports: + _ast + • argparse + • collections + • contextlib + • enum + • inspect + • sys + • warnings + +
+
+imported by: + inspect + +
+ +
+ +
+ + atexit (builtin module)
+imported by: + logging + • multiprocessing.util + • weakref + +
+ +
+ +
+ + base64 +SourceModule
+imports: + binascii + • getopt + • re + • struct + • sys + +
+
+imported by: + email._encoded_words + • email.base64mime + • email.encoders + • encodings.base64_codec + • secrets + • ssl + • urllib.request + • xmlrpc.client + +
+ +
+ +
+ + binascii /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/binascii.cpython-310-x86_64-linux-gnu.so
+imported by: + base64 + • email._encoded_words + • email.base64mime + • email.contentmanager + • email.header + • encodings.hex_codec + • encodings.uu_codec + • quopri + • secrets + • uu + • zipfile + +
+ +
+ +
+ + bisect +SourceModule
+imports: + _bisect + +
+
+imported by: + multiprocessing.heap + • random + • statistics + • urllib.request + +
+ +
+ +
+ + builtins (builtin module)
+imported by: + bz2 + • codecs + • dataclasses + • gettext + • gzip + • inspect + • locale + • lzma + • operator + • reprlib + • subprocess + • tarfile + • tokenize + • warnings + +
+ +
+ +
+ + bz2 +SourceModule
+imports: + _bz2 + • _compression + • builtins + • io + • os + +
+
+imported by: + encodings.bz2_codec + • shutil + • tarfile + • zipfile + +
+ +
+ +
+ + calendar +SourceModule
+imports: + argparse + • datetime + • itertools + • locale + • sys + +
+
+imported by: + _strptime + • email._parseaddr + • http.cookiejar + • ssl + +
+ +
+ +
+ + codecs +SourceModule
+imports: + _codecs + • builtins + • encodings + • sys + +
+
+imported by: + _pickle + • encodings + • encodings.ascii + • encodings.base64_codec + • encodings.big5 + • encodings.big5hkscs + • encodings.bz2_codec + • encodings.charmap + • encodings.cp037 + • encodings.cp1006 + • encodings.cp1026 + • encodings.cp1125 + • encodings.cp1140 + • encodings.cp1250 + • encodings.cp1251 + • encodings.cp1252 + • encodings.cp1253 + • encodings.cp1254 + • encodings.cp1255 + • encodings.cp1256 + • encodings.cp1257 + • encodings.cp1258 + • encodings.cp273 + • encodings.cp424 + • encodings.cp437 + • encodings.cp500 + • encodings.cp720 + • encodings.cp737 + • encodings.cp775 + • encodings.cp850 + • encodings.cp852 + • encodings.cp855 + • encodings.cp856 + • encodings.cp857 + • encodings.cp858 + • encodings.cp860 + • encodings.cp861 + • encodings.cp862 + • encodings.cp863 + • encodings.cp864 + • encodings.cp865 + • encodings.cp866 + • encodings.cp869 + • encodings.cp874 + • encodings.cp875 + • encodings.cp932 + • encodings.cp949 + • encodings.cp950 + • encodings.euc_jis_2004 + • encodings.euc_jisx0213 + • encodings.euc_jp + • encodings.euc_kr + • encodings.gb18030 + • encodings.gb2312 + • encodings.gbk + • encodings.hex_codec + • encodings.hp_roman8 + • encodings.hz + • encodings.idna + • encodings.iso2022_jp + • encodings.iso2022_jp_1 + • encodings.iso2022_jp_2 + • encodings.iso2022_jp_2004 + • encodings.iso2022_jp_3 + • encodings.iso2022_jp_ext + • encodings.iso2022_kr + • encodings.iso8859_1 + • encodings.iso8859_10 + • encodings.iso8859_11 + • encodings.iso8859_13 + • encodings.iso8859_14 + • encodings.iso8859_15 + • encodings.iso8859_16 + • encodings.iso8859_2 + • encodings.iso8859_3 + • encodings.iso8859_4 + • encodings.iso8859_5 + • encodings.iso8859_6 + • encodings.iso8859_7 + • encodings.iso8859_8 + • encodings.iso8859_9 + • encodings.johab + • encodings.koi8_r + • encodings.koi8_t + • encodings.koi8_u + • encodings.kz1048 + • encodings.latin_1 + • encodings.mac_arabic + • encodings.mac_croatian + • encodings.mac_cyrillic + • encodings.mac_farsi + • encodings.mac_greek + • encodings.mac_iceland + • encodings.mac_latin2 + • encodings.mac_roman + • encodings.mac_romanian + • encodings.mac_turkish + • encodings.mbcs + • encodings.oem + • encodings.palmos + • encodings.ptcp154 + • encodings.punycode + • encodings.quopri_codec + • encodings.raw_unicode_escape + • encodings.rot_13 + • encodings.shift_jis + • encodings.shift_jis_2004 + • encodings.shift_jisx0213 + • encodings.tis_620 + • encodings.undefined + • encodings.unicode_escape + • encodings.utf_16 + • encodings.utf_16_be + • encodings.utf_16_le + • encodings.utf_32 + • encodings.utf_32_be + • encodings.utf_32_le + • encodings.utf_7 + • encodings.utf_8 + • encodings.utf_8_sig + • encodings.uu_codec + • encodings.zlib_codec + • json + • pickle + • snpkit.py + • tokenize + • xml.sax.saxutils + +
+ +
+ +
+ + collections +Package
+imports: + _collections + • _collections_abc + • _weakref + • copy + • heapq + • itertools + • keyword + • operator + • reprlib + • sys + +
+
+imported by: + _pydecimal + • ast + • collections.abc + • configparser + • contextlib + • dis + • email.feedparser + • functools + • importlib.metadata + • importlib.metadata._collections + • importlib.readers + • inspect + • multiprocessing.heap + • multiprocessing.pool + • multiprocessing.queues + • pkgutil + • pprint + • queue + • selectors + • shlex + • shutil + • snpkit.py + • ssl + • statistics + • string + • threading + • tokenize + • traceback + • typing + • urllib.parse + • urllib.robotparser + +
+ +
+ +
+ + collections.abc +SourceModule
+imports: + _collections_abc + • collections + +
+
+imported by: + configparser + • http.client + • inspect + • logging + • selectors + • snpkit.py + • tracemalloc + • typing + +
+ +
+ +
+ + config_settings +SourceModule
+imported by: + modules.phage_detection + • modules.snpeff + • modules.tabix + • modules.variant_diagnostics.find_repeats + • modules.variant_diagnostics.mask_regions + • snpkit.py + +
+ +
+ +
+ + configparser +SourceModule
+imports: + collections + • collections.abc + • functools + • io + • itertools + • os + • re + • sys + • warnings + +
+
+imported by: + snpkit.py + +
+ +
+ +
+ + contextlib +SourceModule
+imports: + _collections_abc + • abc + • collections + • functools + • sys + • types + +
+
+imported by: + _threading_local + • ast + • getpass + • glob + • importlib.metadata + • importlib.util + • subprocess + • typing + • urllib.request + • zipfile + +
+ +
+ +
+ + contextvars +SourceModule
+imports: + _contextvars + +
+
+imported by: + _pydecimal + +
+ +
+ +
+ + copy +SourceModule
+imports: + 'org.python' + • copyreg + • types + • weakref + +
+
+imported by: + _sre + • argparse + • collections + • dataclasses + • email.generator + • gettext + • http.cookiejar + • tarfile + • weakref + +
+ +
+ +
+ + copyreg +SourceModule
+imports: + functools + • operator + +
+
+imported by: + _pickle + • copy + • multiprocessing.reduction + • pickle + • re + • snpkit.py + +
+ +
+ +
+ + csv +SourceModule
+imports: + _csv + • io + • re + +
+
+imported by: + importlib.metadata + +
+ +
+ +
+ + ctypes +Package
+imports: + _ctypes + • ctypes._endian + • nt + • os + • struct + • sys + • types + +
+
+imported by: + ctypes._endian + • multiprocessing.sharedctypes + +
+ +
+ +
+ + ctypes._endian +SourceModule
+imports: + ctypes + • sys + +
+
+imported by: + ctypes + +
+ +
+ +
+ + dataclasses +SourceModule
+imports: + _thread + • abc + • builtins + • copy + • functools + • inspect + • keyword + • re + • sys + • types + +
+
+imported by: + pprint + +
+ +
+ +
+ + datetime +SourceModule
+imports: + _datetime + • _strptime + • math + • operator + • sys + • time + +
+
+imported by: + _strptime + • calendar + • email.utils + • http.cookiejar + • log_modules + • modules.log_modules + • snpkit.py + • xmlrpc.client + +
+ +
+ +
+ + decimal +SourceModule
+imports: + _decimal + • _pydecimal + +
+
+imported by: + fractions + • statistics + • xmlrpc.client + +
+ +
+ +
+ + dis +SourceModule
+imports: + argparse + • collections + • io + • opcode + • sys + • types + +
+
+imported by: + inspect + +
+ +
+ +
+ + email +Package
+imports: + email._header_value_parser + • email.charset + • email.errors + • email.header + • email.parser + +
+
+imported by: + email._encoded_words + • email._header_value_parser + • email._parseaddr + • email._policybase + • email.base64mime + • email.charset + • email.contentmanager + • email.encoders + • email.errors + • email.feedparser + • email.generator + • email.header + • email.headerregistry + • email.iterators + • email.message + • email.parser + • email.policy + • email.quoprimime + • email.utils + • importlib.metadata + • urllib.request + +
+ +
+ +
+ + email._encoded_words +SourceModule
+imports: + base64 + • binascii + • email + • email.errors + • functools + • re + • string + +
+
+imported by: + email._header_value_parser + • email.message + +
+ +
+ +
+ + email._header_value_parser +SourceModule
+imports: + email + • email._encoded_words + • email.errors + • email.utils + • operator + • re + • string + • sys + • urllib + +
+
+imported by: + email + • email.headerregistry + +
+ +
+ +
+ + email._parseaddr +SourceModule
+imports: + calendar + • email + • time + +
+
+imported by: + email.utils + +
+ +
+ +
+ + email._policybase +SourceModule
+imports: + abc + • email + • email.charset + • email.header + • email.utils + +
+
+imported by: + email.feedparser + • email.message + • email.parser + • email.policy + +
+ +
+ +
+ + email.base64mime +SourceModule
+imports: + base64 + • binascii + • email + +
+
+imported by: + email.charset + • email.header + +
+ +
+ +
+ + email.charset +SourceModule
+imports: + email + • email.base64mime + • email.encoders + • email.errors + • email.quoprimime + • functools + +
+
+imported by: + email + • email._policybase + • email.contentmanager + • email.header + • email.message + • email.utils + +
+ +
+ +
+ + email.contentmanager +SourceModule
+imports: + binascii + • email + • email.charset + • email.errors + • email.message + • email.quoprimime + +
+
+imported by: + email.policy + +
+ +
+ +
+ + email.encoders +SourceModule
+imports: + base64 + • email + • quopri + +
+
+imported by: + email.charset + +
+ +
+ +
+ + email.errors +SourceModule
+imports: + email + +
+
+imported by: + email + • email._encoded_words + • email._header_value_parser + • email.charset + • email.contentmanager + • email.feedparser + • email.header + • email.headerregistry + • email.message + +
+ +
+ +
+ + email.feedparser +SourceModule
+imports: + collections + • email + • email._policybase + • email.errors + • email.message + • io + • re + +
+
+imported by: + email.parser + +
+ +
+ +
+ + email.generator +SourceModule
+imports: + copy + • email + • email.utils + • io + • random + • re + • sys + • time + +
+
+imported by: + email.message + +
+ +
+ +
+ + email.header +SourceModule
+imports: + binascii + • email + • email.base64mime + • email.charset + • email.errors + • email.quoprimime + • re + +
+
+imported by: + email + • email._policybase + +
+ +
+ +
+ + email.headerregistry +SourceModule
+imports: + email + • email._header_value_parser + • email.errors + • email.utils + • types + +
+
+imported by: + email.policy + +
+ +
+ +
+ + email.iterators +SourceModule
+imports: + email + • io + • sys + +
+
+imported by: + email.message + +
+ +
+ +
+ + email.message +SourceModule
+imports: + email + • email._encoded_words + • email._policybase + • email.charset + • email.errors + • email.generator + • email.iterators + • email.policy + • email.utils + • io + • quopri + • re + • uu + +
+
+imported by: + email.contentmanager + • email.feedparser + • email.policy + • http.client + • importlib.metadata._adapters + +
+ +
+ +
+ + email.parser +SourceModule
+imports: + email + • email._policybase + • email.feedparser + • io + +
+
+imported by: + email + • http.client + +
+ +
+ +
+ + email.policy +SourceModule
+imports: + email + • email._policybase + • email.contentmanager + • email.headerregistry + • email.message + • email.utils + • re + • sys + +
+
+imported by: + email.message + +
+ +
+ +
+ + email.quoprimime +SourceModule
+imports: + email + • re + • string + +
+
+imported by: + email.charset + • email.contentmanager + • email.header + +
+ +
+ +
+ + email.utils +SourceModule
+imports: + datetime + • email + • email._parseaddr + • email.charset + • os + • random + • re + • socket + • time + • urllib.parse + +
+
+imported by: + email._header_value_parser + • email._policybase + • email.generator + • email.headerregistry + • email.message + • email.policy + • urllib.request + +
+ +
+ +
+ + encodings +Package
+imports: + _winapi + • codecs + • encodings + • encodings.aliases + • encodings.ascii + • encodings.base64_codec + • encodings.big5 + • encodings.big5hkscs + • encodings.bz2_codec + • encodings.charmap + • encodings.cp037 + • encodings.cp1006 + • encodings.cp1026 + • encodings.cp1125 + • encodings.cp1140 + • encodings.cp1250 + • encodings.cp1251 + • encodings.cp1252 + • encodings.cp1253 + • encodings.cp1254 + • encodings.cp1255 + • encodings.cp1256 + • encodings.cp1257 + • encodings.cp1258 + • encodings.cp273 + • encodings.cp424 + • encodings.cp437 + • encodings.cp500 + • encodings.cp720 + • encodings.cp737 + • encodings.cp775 + • encodings.cp850 + • encodings.cp852 + • encodings.cp855 + • encodings.cp856 + • encodings.cp857 + • encodings.cp858 + • encodings.cp860 + • encodings.cp861 + • encodings.cp862 + • encodings.cp863 + • encodings.cp864 + • encodings.cp865 + • encodings.cp866 + • encodings.cp869 + • encodings.cp874 + • encodings.cp875 + • encodings.cp932 + • encodings.cp949 + • encodings.cp950 + • encodings.euc_jis_2004 + • encodings.euc_jisx0213 + • encodings.euc_jp + • encodings.euc_kr + • encodings.gb18030 + • encodings.gb2312 + • encodings.gbk + • encodings.hex_codec + • encodings.hp_roman8 + • encodings.hz + • encodings.idna + • encodings.iso2022_jp + • encodings.iso2022_jp_1 + • encodings.iso2022_jp_2 + • encodings.iso2022_jp_2004 + • encodings.iso2022_jp_3 + • encodings.iso2022_jp_ext + • encodings.iso2022_kr + • encodings.iso8859_1 + • encodings.iso8859_10 + • encodings.iso8859_11 + • encodings.iso8859_13 + • encodings.iso8859_14 + • encodings.iso8859_15 + • encodings.iso8859_16 + • encodings.iso8859_2 + • encodings.iso8859_3 + • encodings.iso8859_4 + • encodings.iso8859_5 + • encodings.iso8859_6 + • encodings.iso8859_7 + • encodings.iso8859_8 + • encodings.iso8859_9 + • encodings.johab + • encodings.koi8_r + • encodings.koi8_t + • encodings.koi8_u + • encodings.kz1048 + • encodings.latin_1 + • encodings.mac_arabic + • encodings.mac_croatian + • encodings.mac_cyrillic + • encodings.mac_farsi + • encodings.mac_greek + • encodings.mac_iceland + • encodings.mac_latin2 + • encodings.mac_roman + • encodings.mac_romanian + • encodings.mac_turkish + • encodings.mbcs + • encodings.oem + • encodings.palmos + • encodings.ptcp154 + • encodings.punycode + • encodings.quopri_codec + • encodings.raw_unicode_escape + • encodings.rot_13 + • encodings.shift_jis + • encodings.shift_jis_2004 + • encodings.shift_jisx0213 + • encodings.tis_620 + • encodings.undefined + • encodings.unicode_escape + • encodings.utf_16 + • encodings.utf_16_be + • encodings.utf_16_le + • encodings.utf_32 + • encodings.utf_32_be + • encodings.utf_32_le + • encodings.utf_7 + • encodings.utf_8 + • encodings.utf_8_sig + • encodings.uu_codec + • encodings.zlib_codec + • sys + +
+
+imported by: + codecs + • encodings + • encodings.aliases + • encodings.ascii + • encodings.base64_codec + • encodings.big5 + • encodings.big5hkscs + • encodings.bz2_codec + • encodings.charmap + • encodings.cp037 + • encodings.cp1006 + • encodings.cp1026 + • encodings.cp1125 + • encodings.cp1140 + • encodings.cp1250 + • encodings.cp1251 + • encodings.cp1252 + • encodings.cp1253 + • encodings.cp1254 + • encodings.cp1255 + • encodings.cp1256 + • encodings.cp1257 + • encodings.cp1258 + • encodings.cp273 + • encodings.cp424 + • encodings.cp437 + • encodings.cp500 + • encodings.cp720 + • encodings.cp737 + • encodings.cp775 + • encodings.cp850 + • encodings.cp852 + • encodings.cp855 + • encodings.cp856 + • encodings.cp857 + • encodings.cp858 + • encodings.cp860 + • encodings.cp861 + • encodings.cp862 + • encodings.cp863 + • encodings.cp864 + • encodings.cp865 + • encodings.cp866 + • encodings.cp869 + • encodings.cp874 + • encodings.cp875 + • encodings.cp932 + • encodings.cp949 + • encodings.cp950 + • encodings.euc_jis_2004 + • encodings.euc_jisx0213 + • encodings.euc_jp + • encodings.euc_kr + • encodings.gb18030 + • encodings.gb2312 + • encodings.gbk + • encodings.hex_codec + • encodings.hp_roman8 + • encodings.hz + • encodings.idna + • encodings.iso2022_jp + • encodings.iso2022_jp_1 + • encodings.iso2022_jp_2 + • encodings.iso2022_jp_2004 + • encodings.iso2022_jp_3 + • encodings.iso2022_jp_ext + • encodings.iso2022_kr + • encodings.iso8859_1 + • encodings.iso8859_10 + • encodings.iso8859_11 + • encodings.iso8859_13 + • encodings.iso8859_14 + • encodings.iso8859_15 + • encodings.iso8859_16 + • encodings.iso8859_2 + • encodings.iso8859_3 + • encodings.iso8859_4 + • encodings.iso8859_5 + • encodings.iso8859_6 + • encodings.iso8859_7 + • encodings.iso8859_8 + • encodings.iso8859_9 + • encodings.johab + • encodings.koi8_r + • encodings.koi8_t + • encodings.koi8_u + • encodings.kz1048 + • encodings.latin_1 + • encodings.mac_arabic + • encodings.mac_croatian + • encodings.mac_cyrillic + • encodings.mac_farsi + • encodings.mac_greek + • encodings.mac_iceland + • encodings.mac_latin2 + • encodings.mac_roman + • encodings.mac_romanian + • encodings.mac_turkish + • encodings.mbcs + • encodings.oem + • encodings.palmos + • encodings.ptcp154 + • encodings.punycode + • encodings.quopri_codec + • encodings.raw_unicode_escape + • encodings.rot_13 + • encodings.shift_jis + • encodings.shift_jis_2004 + • encodings.shift_jisx0213 + • encodings.tis_620 + • encodings.undefined + • encodings.unicode_escape + • encodings.utf_16 + • encodings.utf_16_be + • encodings.utf_16_le + • encodings.utf_32 + • encodings.utf_32_be + • encodings.utf_32_le + • encodings.utf_7 + • encodings.utf_8 + • encodings.utf_8_sig + • encodings.uu_codec + • encodings.zlib_codec + • locale + • snpkit.py + +
+ +
+ +
+ + encodings.aliases +SourceModule
+imports: + encodings + +
+
+imported by: + encodings + • locale + • snpkit.py + +
+ +
+ +
+ + encodings.ascii +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.base64_codec +SourceModule
+imports: + base64 + • codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.big5 +SourceModule
+imports: + _codecs_tw + • _multibytecodec + • codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.big5hkscs +SourceModule
+imports: + _codecs_hk + • _multibytecodec + • codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.bz2_codec +SourceModule
+imports: + bz2 + • codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.charmap +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp037 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1006 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1026 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1125 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1140 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1250 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1251 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1252 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1253 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1254 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1255 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1256 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1257 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp1258 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp273 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp424 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp437 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp500 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp720 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
+ +
+ +
+ + encodings.cp737 +SourceModule
+imports: + codecs + • encodings + +
+
+imported by: + encodings + • snpkit.py + +
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+
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+
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+
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+
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+ +
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+
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+
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+ +
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+
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+ +
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+
+imported by: + shutil + • tarfile + • zipfile + +
+ +
+ +
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+ +
+ +
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+ +
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+
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+ +
+ +
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+ +
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+
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+ +
+ +
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+
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+ +
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+
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+ +
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+
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+
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+
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+
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+
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+
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+ +
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+ +
+ +
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+ +
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+
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+ +
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+
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+
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+
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+
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+
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+ +
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+
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+ +
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+
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+
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+
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+ +
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+ +
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+
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+
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+
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+
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+
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+
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+ +
+ + zipimport +SourceModule
+imports: + _frozen_importlib + • _frozen_importlib_external + • _imp + • _io + • _warnings + • importlib.readers + • marshal + • os + • sys + • time + • zlib + +
+
+imported by: + pkgutil + +
+ +
+ +
+ + zlib /sw/pkgs/arc/python/3.10.4/lib/python3.10/lib-dynload/zlib.cpython-310-x86_64-linux-gnu.so
+imported by: + encodings.zlib_codec + • gzip + • shutil + • tarfile + • zipfile + • zipimport + +
+ +
+ + + diff --git a/dist/snpkit b/dist/snpkit new file mode 100755 index 0000000..623599c Binary files /dev/null and b/dist/snpkit differ diff --git a/modules/analyze_readdepth_signal_across_genome.py b/modules/analyze_readdepth_signal_across_genome.py new file mode 100644 index 0000000..23024cb --- /dev/null +++ b/modules/analyze_readdepth_signal_across_genome.py @@ -0,0 +1,76 @@ +from __future__ import division +__author__ = 'alipirani' +import os +import readline +import argparse +from itertools import islice +import subprocess +import numpy as np +import pandas as pd +import glob + + +# Parse Command line Arguments +parser = argparse.ArgumentParser(description='Extract Read Depth signal across the genome from GATK Depth of Coverage file') +required = parser.add_argument_group('Required arguments') +optional = parser.add_argument_group('Optional arguments') +required.add_argument('-depth', action='store', dest="depth", + help='Read Depth coverage file generated by GATK Depth of Coverage.') +args = parser.parse_args() + + + +def generate_depth_dataframe(list_of_files): + for file in list_of_files: + print "Analyzing file - %s" % file + df = pd.read_csv("%s" % file, sep='\t', header=0) + n = 100 + count = 0 + fp = open(file.replace('_depth_of_coverage', '_depth_of_coverage_window_mean.txt'), 'w+') + fp.write('%s_Mean_1000bp\n' % os.path.basename(file)) + fp1 = open('window.txt', 'w+') + fp1.write('Window\n') + df = df.groupby(np.arange(len(df['Total_Depth']))//n).mean() + for index, row in df.iterrows(): + count = count + 1 + fp1.write(str(count) + '\n') + fp.write(str(int(row[0])) + '\n') + fp.close() + fp1.close() + paste_command = "paste window.txt" + for file in list_of_files: + paste_command = paste_command + " " + file.replace('_depth_of_coverage', '_depth_of_coverage_window_mean.txt') + paste_command = paste_command + " > Mean_Depth_of_coverage_matrix.tsv" + print (paste_command) + os.system(paste_command) + +def generate_depth_dataframe_Plasmid_SUR(list_of_files): + + gene_lis + + for file in list_of_files: + print "Analyzing file - %s" % file + df = pd.read_csv("%s" % file, sep='\t', header=0) + n = 100 + count = 0 + fp = open(file.replace('_depth_of_coverage', '_depth_of_coverage_window_mean.txt'), 'w+') + fp.write('%s_Mean_1000bp\n' % os.path.basename(file)) + fp1 = open('window.txt', 'w+') + fp1.write('Window\n') + df = df.groupby(np.arange(len(df['Total_Depth']))//n).mean() + for index, row in df.iterrows(): + count = count + 1 + fp1.write(str(count) + '\n') + fp.write(str(int(row[0])) + '\n') + fp.close() + fp1.close() + paste_command = "paste window.txt" + for file in list_of_files: + paste_command = paste_command + " " + file.replace('_depth_of_coverage', '_depth_of_coverage_window_mean.txt') + paste_command = paste_command + " > Mean_Depth_of_coverage_matrix.tsv" + print (paste_command) + os.system(paste_command) + +list_of_files = sorted(glob.glob(args.depth + "/*/*/*_depth_of_coverage")) +print (list_of_files) +generate_depth_dataframe(list_of_files) diff --git a/modules/gatk.py b/modules/gatk.py index 55d55bb..250c744 100755 --- a/modules/gatk.py +++ b/modules/gatk.py @@ -179,6 +179,7 @@ def gatk_DepthOfCoverage(out_sorted_bam, out_path, analysis_name, reference, log pattern = re.compile("|".join(rep.keys())) interval = pattern.sub(lambda m: rep[re.escape(m.group(0))], reference) cmd = "gatk DepthOfCoverage -R %s -O %s/%s_depth_of_coverage -I %s --summary-coverage-threshold 1 --summary-coverage-threshold 5 --summary-coverage-threshold 9 --summary-coverage-threshold 10 --summary-coverage-threshold 15 --summary-coverage-threshold 20 --summary-coverage-threshold 25 --ignore-deletion-sites --intervals %s" % (reference, out_path, analysis_name, out_sorted_bam, interval) + print(cmd) try: call(cmd, logger) except sp.CalledProcessError: diff --git a/pipeline.py b/pipeline.py index cf2bdf0..008d86f 100755 --- a/pipeline.py +++ b/pipeline.py @@ -221,15 +221,15 @@ def stats(): if len(steps_list) == 1: if steps_list[0] == "call": - #clean() - #out_sam = align_reads() - #out_sorted_bam = post_align(out_sam) + clean() + out_sam = align_reads() + out_sorted_bam = post_align(out_sam) out_sorted_bam = "%s/%s_aln_sort.bam" % (args.output_folder, args.analysis_name) #coverage_depth_stats() gatk_depth_of_coverage_file = "%s/%s_depth_of_coverage.sample_summary" % (args.output_folder, args.analysis_name) - ## if not os.path.exists(gatk_depth_of_coverage_file): - ## gatk_depth_of_coverage_file = coverage_depth_stats() - #final_raw_vcf, final_raw_indel_vcf = varcall() + if not os.path.exists(gatk_depth_of_coverage_file): + gatk_depth_of_coverage_file = coverage_depth_stats() + final_raw_vcf, final_raw_indel_vcf = varcall() final_raw_vcf = "%s/%s_aln_mpileup_raw.vcf_5bp_indel_removed.vcf" % (args.output_folder, args.analysis_name) filter(gatk_depth_of_coverage_file) annotation((final_raw_vcf).replace('_aln_mpileup_raw.vcf_5bp_indel_removed.vcf', '_filter2_final.vcf_no_proximate_snp.vcf')) diff --git a/snpkit b/snpkit new file mode 100755 index 0000000..623599c Binary files /dev/null and b/snpkit differ diff --git a/snpkit.py b/snpkit.py index aa729a8..669b172 100755 --- a/snpkit.py +++ b/snpkit.py @@ -1,3 +1,4 @@ +#!/usr/bin/env python3 __author__ = 'alipirani' import sys import os diff --git a/snpkit.spec b/snpkit.spec new file mode 100644 index 0000000..17a8c15 --- /dev/null +++ b/snpkit.spec @@ -0,0 +1,44 @@ +# -*- mode: python ; coding: utf-8 -*- + + +block_cipher = None + + +a = Analysis( + ['snpkit.py'], + pathex=[], + binaries=[], + datas=[], + hiddenimports=[], + hookspath=[], + hooksconfig={}, + runtime_hooks=[], + excludes=[], + win_no_prefer_redirects=False, + win_private_assemblies=False, + cipher=block_cipher, + noarchive=False, +) +pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher) + +exe = EXE( + pyz, + a.scripts, + a.binaries, + a.zipfiles, + a.datas, + [], + name='snpkit', + debug=False, + bootloader_ignore_signals=False, + strip=False, + upx=True, + upx_exclude=[], + runtime_tmpdir=None, + console=True, + disable_windowed_traceback=False, + argv_emulation=False, + target_arch=None, + codesign_identity=None, + entitlements_file=None, +)