aldepyde 0.0.0a32__tar.gz → 0.0.0a35__tar.gz

{aldepyde-0.0.0a32 → aldepyde-0.0.0a35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aldepyde
-Version: 0.0.0a32
+Version: 0.0.0a35
 Summary: A package of chemistry and biochemical tools
 Author-email: Nate McMurray <nate.mcmurray13@gmail.com>
 License: MIT License

{aldepyde-0.0.0a32 → aldepyde-0.0.0a35}/aldepyde/__init__.py

@@ -17,25 +17,6 @@ def get_cache() -> CacheManager:
     global _cache_manager
     return _cache_manager
 
-# def get_cache() -> _cache_handler:
-#     global _cache
-#     # if _cache.null:
-#     #     return create_cache()
-#     return _cache
-
-# def SaveConfig(path: str="config.json", indent: str = "") -> None:
-#     global _config
-#     get_config().Save(path=path, indent=indent)
-#
-#
-# def LoadConfig(s: dict | str, ignore_missing=False) -> None:
-#     global _config
-#     get_config().Load(s, ignore_missing=ignore_missing)
-
-
-# from . import rand
-# from . import biomolecule
-# from . import fetcher
 
 from importlib import import_module
 

{aldepyde-0.0.0a32 → aldepyde-0.0.0a35}/aldepyde/biomolecule/__init__.py

@@ -13,3 +13,6 @@ __all__ =  list(set(_amino_acid.__all__.copy()) |
            set(_pdb.__all__.copy()) |
            set(_rna.__all__.copy()))
 
+import sys
+
+sys.stderr.write("Note that the `biomolecule` submodule is not yet fully tested and may be unstable")

aldepyde-0.0.0a35/aldepyde/databases/SCOPe_Astral.py

@@ -0,0 +1,71 @@
+from aldepyde.databases._database import local_database
+import operator
+from contextlib import nullcontext
+import re
+
+class scop_parser(local_database):
+    op = {
+        "and": lambda a,b,c: a and b and c,
+        "or": lambda a,b,c: a or b or c
+    }
+
+    def fetch(self, url):
+        pass
+
+    def fetch_code(self, codes):
+        pass
+
+    def parse(self, text):
+        pass
+
+    def extract_all_scop(self):
+        pass
+
+    def partition_scope(self):
+        pass
+
+    def extract_all_astral(self):
+        lines = self.fp.readlines()
+        entry = b""
+        for line in lines:
+            if line.startswith(b">") and len(entry) > 0:
+                yield entry
+                entry = b""
+            entry += line
+        yield entry
+
+    # TODO allow a list of search parameters. Big challenge to make efficient, but could be cute
+    def partition_astral(self, destination:None|str=None, append=False, class_name:str=b'',contains_id:str=b'' , contains_desc:str=b'', mode="and") -> dict:
+        mode = mode.lower()
+        # Everything is a byte string in order to play nicely with future parent methods
+        if isinstance(class_name, str):
+            class_name = class_name.encode('utf-8')
+        if isinstance(contains_desc, str):
+            contains_desc = contains_desc.encode('utf-8')
+        if isinstance(contains_id, str):
+            contains_id = contains_id.encode('utf-8')
+        if mode != "and" and mode != "or":
+            raise ValueError("mode must be \"and\" or \"or\".")
+        logic = scop_parser.op[mode]
+        regex = re.compile(b">[a-zA-Z0-9_.]* *[a-l](.[0-9]+)?(.[0-9]+)?(.[0-9]+)?")
+        if append:
+            file_context = open(destination, 'ab') if destination is not None else nullcontext()
+        else:
+            file_context = open(destination, 'wb') if destination is not None else nullcontext()
+        with file_context as fp:
+            ret_dict = dict()
+            for line in self.extract_all_astral():
+                identifiers = regex.search(line).group().split()
+                id = identifiers[0]
+                cls = identifiers[1]
+                unmatched_spl = regex.sub(b'', line).split(b'\n')
+                desc = unmatched_spl[0]
+                sequence = unmatched_spl[1:]
+                if logic(class_name.lower() in cls.lower(), contains_id.lower() in id.lower(), contains_desc.lower() in desc.lower()):
+                    ret_dict[id] = { # Yes, I know '>' isn't part of the FASTA identifier. This keeps things more consistant
+                        "class" : cls,
+                        "description" : desc,
+                        "sequence" : b"".join(sequence)
+                    }
+                    fp.write(line)
+        return ret_dict

aldepyde-0.0.0a35/aldepyde/databases/UniRef.py

@@ -0,0 +1,114 @@
+import zlib
+from aldepyde.databases._database import streamable_database
+from aldepyde.utils import ProgressBar
+
+class uniref_parser(streamable_database):
+    def __init__(self):
+        super().__init__()
+
+    # TODO single entry parsing
+    # TODO store metadata upon request
+    # TODO implement abstract methods
+
+    @staticmethod
+    def stream_uniref_gz(filepath, chunk_size=8192, use_progress_bar=False, stitch=False):
+        raw_stream, size = streamable_database.open_stream(filepath)
+        pbar = ProgressBar(size//chunk_size) if use_progress_bar else None
+        decompressor = zlib.decompressobj(16 + zlib.MAX_WBITS)
+        try:
+            if not stitch:
+                while True:
+                    comp_chunk = raw_stream.read(chunk_size)
+                    if not comp_chunk:
+                        break
+                    if pbar is not None:
+                        pbar.update()
+                    decomp_chunk = decompressor.decompress(comp_chunk)
+                    if decomp_chunk:
+                        yield decomp_chunk
+                final = decompressor.flush()
+                if final:
+                    yield final
+            else:
+                # Really hacky solution for now
+                # TODO Clean this up
+                yield from uniref_parser.stitch_streamed_sequences(
+                    uniref_parser.stream_uniref_gz(filepath=filepath, chunk_size=chunk_size, use_progress_bar=use_progress_bar, stitch=False))
+        finally:
+            raw_stream.close()
+
+    @staticmethod
+    def download_file(url, destination, chunk_size=8192, use_progress_bar=False):
+        raw_stream, size = streamable_database.open_stream(url)
+        pbar = ProgressBar(size // chunk_size) if use_progress_bar else None
+        with open(destination, 'wb') as fp:
+            while True:
+                chunk = raw_stream.read(chunk_size)
+                if not chunk:
+                    break
+                if pbar is not None:
+                    pbar.update()
+                fp.write(chunk)
+
+
+    @staticmethod
+    def stitch_streamed_sequences(stream, as_str=True):
+        buffer = b''
+        for chunk in stream:
+            buffer += chunk
+            while buffer.count(b'>') >= 2:
+                sequences = [b">" + seq for seq in buffer.split(b">") if seq != b""]
+                buffer = buffer[buffer.rfind(b">"):]
+                ret_l = [b"".join(sequence.split(b'\n')[1:]).replace(b"\n", b"") for sequence in sequences[:-1]]
+                for s in ret_l:
+                    yield s if not as_str else s.decode()
+        yield uniref_parser._final_sequence(buffer) if not as_str else uniref_parser._final_sequence(buffer).decode()
+
+    @staticmethod
+    def _final_sequence(buffer):
+        lines = buffer.split(b'\n')
+        return b"".join(lines[1:])
+
+    @staticmethod
+    def stream_uniref50(chunk_size=8192, use_progress_bar=False, stitch=False):
+        if not stitch:
+            yield from uniref_parser.stream_uniref_gz('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz',
+                                                  chunk_size=chunk_size, use_progress_bar=use_progress_bar)
+        else:
+            yield from uniref_parser.stitch_streamed_sequences(uniref_parser.stream_uniref_gz(
+                'https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz',
+                                                  chunk_size=chunk_size, use_progress_bar=use_progress_bar))
+
+    @staticmethod
+    def stream_uniref90(chunk_size=8192, use_progress_bar=False, stitch=False):
+        if not stitch:
+            yield from uniref_parser.stream_uniref_gz('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz',
+                                                  chunk_size=chunk_size, use_progress_bar=use_progress_bar)
+        else:
+            yield from uniref_parser.stitch_streamed_sequences(uniref_parser.stream_uniref_gz(
+                'https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz',
+                chunk_size=chunk_size, use_progress_bar=use_progress_bar))
+
+    @staticmethod
+    def stream_uniref100(chunk_size=8192, use_progress_bar=False, stitch=False):
+        if not stitch:
+            yield from uniref_parser.stream_uniref_gz('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz',
+                                                  chunk_size=chunk_size, use_progress_bar=use_progress_bar)
+        else:
+            yield from uniref_parser.stitch_streamed_sequences(uniref_parser.stream_uniref_gz(
+                'https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz',
+                chunk_size=chunk_size, use_progress_bar=use_progress_bar))
+
+    @staticmethod
+    def download_uniref50(destination='uniref50.fasta.gz', chunk_size=8192, use_progress_bar=False):
+        uniref_parser.download_file('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz', destination=destination,
+                                    chunk_size=chunk_size, use_progress_bar=use_progress_bar)
+
+    @staticmethod
+    def download_uniref90(destination='uniref90.fasta.gz', chunk_size=8192, use_progress_bar=False):
+        uniref_parser.download_file('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz', destination=destination,
+                                    chunk_size=chunk_size, use_progress_bar=use_progress_bar)
+    @staticmethod
+    def download_uniref100(destination='uniref100.fasta.gz', chunk_size=8192, use_progress_bar=False):
+        uniref_parser.download_file('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz', destination=destination,
+                                    chunk_size=chunk_size, use_progress_bar=use_progress_bar)

aldepyde-0.0.0a35/aldepyde/databases/_database.py

@@ -0,0 +1,72 @@
+from abc import ABC, abstractmethod
+import gzip
+import requests
+import os
+from typing import Tuple, BinaryIO
+from io import TextIOWrapper
+
+class streamable_database(ABC):
+
+    def __init__(self):
+        pass
+
+    @abstractmethod
+    def fetch(self, url):
+        pass
+
+    @abstractmethod
+    def fetch_code(self, codes):
+        pass
+
+    @abstractmethod
+    def parse(self, text):
+        pass
+
+    @staticmethod
+    def open_stream(source:str) -> Tuple[BinaryIO, int] | None:
+        if source.startswith('http://') or source.startswith('https://'):
+            resp = requests.get(source, stream=True)
+            resp.raise_for_status()
+            length = resp.headers.get("Content-Length")
+            return resp.raw, int(length) if length else None
+        else:
+            size = os.path.getsize(source)
+            return open(source, 'rb'), size
+
+
+
+    # Yes, I know the first conditionals do the same thing
+
+    def __call__(self):
+        pass
+
+class local_database(ABC):
+
+    def __init__(self, filepath=None, as_fp=False):
+        self.fp = None
+        self.as_fp = as_fp
+        self.size = None
+        self.load_path(filepath)
+
+    def load_path(self, filepath):
+        self.filepath = filepath
+
+    def get_pointer(self):
+        return self.fp
+
+    def __enter__(self):
+        self.fp, self.size = local_database.open_stream(self.filepath)
+        if self.as_fp:
+            return self.fp
+        else:
+            return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        if self.fp is not None:
+            self.fp.close()
+        self.fp = None
+
+    @staticmethod
+    def open_stream(source:str) -> Tuple[BinaryIO, int] | None:
+        size = os.path.getsize(source)
+        return open(source, 'rb'), size

{aldepyde-0.0.0a32 → aldepyde-0.0.0a35}/aldepyde/rand/RandomProtein.py

@@ -11,6 +11,8 @@ class InvalidDistribution(Exception):
 class ImpossibleSetting(Exception):
     pass
 
+
+# TODO This whole thing needs to be cleaned up to better align with more modern python
 class RandomProtein:
     # Hardcode data for now
     def __init__(self, His_Is_Charged=True, Cys_Is_Polar=True, Charged_Is_Polar=True, Distribution="Swiss"):

aldepyde-0.0.0a35/aldepyde/rand/__init__.py

@@ -0,0 +1,6 @@
+from aldepyde.rand.RandomProtein import *
+
+__all__ = ['RandomProtein']
+
+import sys
+sys.stderr.write("Note that the `rand` submodule is not yet fully tested and may be unstable")

{aldepyde-0.0.0a32 → aldepyde-0.0.0a35}/aldepyde.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aldepyde
-Version: 0.0.0a32
+Version: 0.0.0a35
 Summary: A package of chemistry and biochemical tools
 Author-email: Nate McMurray <nate.mcmurray13@gmail.com>
 License: MIT License

{aldepyde-0.0.0a32 → aldepyde-0.0.0a35}/aldepyde.egg-info/SOURCES.txt

@@ -31,6 +31,7 @@ aldepyde/data/RemoteFileHandler.py
 aldepyde/data/__init__.py
 aldepyde/databases/PDB.py
 aldepyde/databases/RemoteFileHandler.py
+aldepyde/databases/SCOPe_Astral.py
 aldepyde/databases/UniRef.py
 aldepyde/databases/__init__.py
 aldepyde/databases/_database.py

{aldepyde-0.0.0a32 → aldepyde-0.0.0a35}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 "aldepyde" = ["json/*.json"]
 [project]
 name = "aldepyde"
-version = "0.0.0a32"
+version = "0.0.0a35"
 authors = [
   { name="Nate McMurray", email="nate.mcmurray13@gmail.com" },
 ]

aldepyde-0.0.0a32/aldepyde/databases/UniRef.py

@@ -1,75 +0,0 @@
-import zlib
-
-from aldepyde.databases.RemoteFileHandler import RemoteFileHandler
-from aldepyde.databases._database import _database
-from aldepyde.utils import ProgressBar
-import os
-import gzip
-
-class uniref_parser(_database):
-    def __init__(self):
-        pass
-
-    #TODO Fix the total calculation
-    @staticmethod
-    def stream_uniref_gz(filepath, chunk_size=8192, use_progress_bar=False):
-        if use_progress_bar is not None:
-            raw_stream, size = _database.open_stream(filepath)
-            pbar = ProgressBar(size//chunk_size) if use_progress_bar else None
-            decompressor = zlib.decompressobj(16 + zlib.MAX_WBITS)
-            try:
-                while True:
-                    comp_chunk = raw_stream.read(chunk_size)
-                    if not comp_chunk:
-                        break
-                    if pbar is not None:
-                        pbar.update()
-                    decomp_chunk = decompressor.decompress(comp_chunk)
-                    if decomp_chunk:
-                        yield decomp_chunk
-                final = decompressor.flush()
-                if final:
-                    yield final
-            finally:
-                raw_stream.close()
-
-    @staticmethod
-    def stitch_streamed_sequences(stream, as_str=True):
-        buffer = b''
-        for chunk in stream:
-            buffer += chunk
-            while buffer.count(b'>') >= 2:
-                sequences = [b">" + seq for seq in buffer.split(b">") if seq != b""]
-                buffer = buffer[buffer.rfind(b">"):]
-                ret_l = [b"".join(sequence.split(b'\n')[1:]).replace(b"\n", b"") for sequence in sequences[:-1]]
-                for s in ret_l:
-                    yield s if not as_str else s.decode()
-        yield uniref_parser._final_sequence(buffer) if not as_str else uniref_parser._final_sequence(buffer).decode()
-
-    @staticmethod
-    def _final_sequence(buffer):
-        lines = buffer.split(b'\n')
-        return b"".join(lines[1:])
-
-    @staticmethod
-    def stream_uniref50(chunk_size=8192, use_progress_bar=False):
-        yield from uniref_parser.stream_uniref_gz('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz',
-                                                  chunk_size=chunk_size, use_progress_bar=use_progress_bar)
-        # yield from RemoteFileHandler.stream_url(
-        #         'https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz', chunk_size=chunk_size)
-
-    @staticmethod
-    def stream_uniref90(chunk_size=8192, use_progress_bar=False):
-        yield from uniref_parser.stream_uniref_gz('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz',
-                                                  chunk_size=chunk_size, use_progress_bar=use_progress_bar)
-
-        # yield from RemoteFileHandler.stream_url(
-        #         'https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz', chunk_size=chunk_size)
-
-    @staticmethod
-    def stream_uniref100(chunk_size=8192, use_progress_bar=False):
-        yield from uniref_parser.stream_uniref_gz('https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz',
-                                                  chunk_size=chunk_size, use_progress_bar=use_progress_bar)
-
-        # yield from RemoteFileHandler.stream_url(
-        #         'https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref100/uniref100.fasta.gz', chunk_size=chunk_size)

aldepyde-0.0.0a32/aldepyde/databases/_database.py

@@ -1,38 +0,0 @@
-from abc import ABC, abstractmethod
-import gzip
-import requests
-import os
-from typing import Tuple, BinaryIO
-from io import TextIOWrapper
-
-class _database(ABC):
-
-    @abstractmethod
-    def fetch(self, url):
-        pass
-
-    @abstractmethod
-    def fetch_code(self, codes):
-        pass
-
-    @abstractmethod
-    def parse(self, text):
-        pass
-
-    @staticmethod
-    def open_stream(source:str) -> Tuple[BinaryIO, int] | None:
-        if source.startswith('http://') or source.startswith('https://'):
-            resp = requests.get(source, stream=True)
-            resp.raise_for_status()
-            length = resp.headers.get("Content-Length")
-            return resp.raw, int(length) if length else None
-        else:
-            size = os.path.getsize(source)
-            return open(source, 'rb'), size
-
-
-
-    # Yes, I know the first conditionals do the same thing
-
-    def __call__(self):
-        pass

aldepyde-0.0.0a32/aldepyde/rand/__init__.py

@@ -1,3 +0,0 @@
-from aldepyde.rand.RandomProtein import *
-
-__all__ = ['RandomProtein']