WIP: Motif search

.gitignore

@@ -36,6 +36,7 @@ __pycache__
 
 .pypirc
 .gitignore
+.python-version
 
 chauthorinfo.sh
 pre-commit.sh
@@ -48,3 +49,6 @@ Documentation/*
 *log
 *BAK
 *.sublime*
+*.code-workspace
+.vscode/
+data/

prody/database/__init__.py

@@ -70,6 +70,32 @@
 
 .. _GOA: https://www.ebi.ac.uk/GOA/
 
+Swiss-Prot
+================================
+The following classes and functions can be used to search and retrieve data from the Swiss-Prot database:
+  * :class:`.SwissProt` - class to handle Swiss-Prot data from Expasy
+  * :func:`.getCurrentRelease` - gets current Swiss-Prot release version
+  * :func:`.downloadRelease` - downloads current Swiss-Prot database files
+  * :func:`.saveRelease` - saves new Swiss-Prot release version
+  * :func:`.updateRelease` - updates Swiss-Prot local database
+  * :func:`.getLocalRelease` - checks local Swiss-Prot release version
+  * :func:`.checkForUpdates` - checks wheather there is newer Swiss-Prot version than current local one
+
+  RefSeq
+  ================================
+The following classes and functions can be used to search and retrieve data from the RefSeq database:
+  * :class:` .RefSeq` - class to handle RefSeq data
+  * :func:` getCurrentRelease` - func desc
+  * :func:` getInstalledFiles` - func desc
+  * :func:` saveInstalledFiles` - func desc
+  * :func:` getLocalFiles` - func desc
+  * :func:` getFiles` - func desc
+  * :func:` pepareDownloadFileList` - func desc
+  * :func:` downloadRelease` - func desc
+  * :func:` saveRelease` - func desc
+  * :func:` updateRelease` - func desc
+  * :func:` getLocalRelease` - func desc
+  * :func:` checkForUpdates` - func desc
 
 """
 
@@ -98,3 +124,11 @@
 from . import quartataweb
 from .quartataweb import *
 __all__.extend(quartataweb.__all__)
+
+from . import swissprot
+from .swissprot import *
+__all__.extend(swissprot.__all__)
+
+from . import refseq
+from .refseq import *
+__all__.extend(refseq.__all__)

prody/database/refseq.py

@@ -0,0 +1,160 @@
+# -*- coding: utf-8 -*-
+
+"""RefSeq database operations."""
+
+import os
+import re
+from concurrent.futures import ThreadPoolExecutor
+
+import requests
+from prody import LOGGER
+from prody.utilities.helpers import downloadFile
+from prody.utilities.pathtools import PRODY_DATA
+
+__all__ = ["RefSeq"]
+
+
+class RefSeq:
+    """RefSeq database."""
+
+    RELEASE = "release.txt"
+    CHECK_SUMS = "files_installed.txt"
+
+    @classmethod
+    def getCurrentRelease(cls) -> str:
+        """Get current RefSeq db release version.
+
+        Raises:
+            Exception: No release version found.
+
+        Returns:
+            str: RefSeq db release version.
+        """
+        rs_release = ""
+        url = "https://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER"
+        try:
+            response = requests.get(url)
+        except requests.exceptions.RequestException as exception:
+            LOGGER.error(str(exception))
+        else:
+            rs_release = response.text
+        if not re.match(r"\d+", rs_release):
+            LOGGER.error("Could't determine release version.")
+        LOGGER.debug("RefSeq current release: {}".format(rs_release))
+        return rs_release
+
+    @classmethod
+    def getInstalledFiles(cls) -> str:
+        """Reads installed files with corresponding check sums."""
+        LOGGER.debug("Downloading installed files with check sums.")
+        current_release = cls.getCurrentRelease()
+        url = f"https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release{current_release}.files.installed"
+        try:
+            response = requests.get(url)
+        except requests.exceptions.RequestException as exception:
+            LOGGER.error(str(exception))
+        else:
+            result = ""
+            lines = response.text.split("\n")
+            for line in lines:
+                if re.search(r"complete\.(\d+\.){1,2}protein\.faa\.gz", line):
+                    result += line + "\n"
+            return result
+
+    @classmethod
+    def saveInstalledFiles(cls) -> None:
+        """Saves installed files list with check sums locally."""
+        installed_files = cls.getInstalledFiles()
+        path = os.path.join(PRODY_DATA, cls.__name__)
+        os.makedirs(path, exist_ok=True)
+        with open(f"{PRODY_DATA}/{cls.__name__}/{cls.CHECK_SUMS}", "w", encoding="utf-8") as file:
+            file.write(installed_files)
+        LOGGER.debug(f"{cls.CHECK_SUMS} file saved locally.")
+
+    @classmethod
+    def getLocalFiles(cls) -> dict:
+        """Lists local RefSeq FASTA protein files and corresponding check sums.
+
+        Returns:
+            dict: file names and corresponding check sums.
+        """
+        LOGGER.debug("Getting local RefSeq protein FASTA files")
+        path = os.path.join(PRODY_DATA, cls.__name__)
+        os.makedirs(path, exist_ok=True)
+        with open(f"{PRODY_DATA}/{cls.__name__}/{cls.CHECK_SUMS}", "r", encoding="utf-8") as file:
+            text = file.read()
+            results = re.findall(r"^(\d+)\s+(\S+)$", text, re.M)
+            return {result[1]: result[0] for result in results}
+
+    @classmethod
+    def getFiles(cls) -> dict:
+        """Lists all FASTA protein files on RefSeq ftp server.
+
+        Returns:
+            dict: FASTA protein files with check sums.
+        """
+        LOGGER.debug("Getting protein FASTA file list from RefSeq.")
+        installed_files = cls.getInstalledFiles()
+        file_matcher = re.compile(r"^(\d+)\s+(\S+)$", re.M)
+        files = re.findall(file_matcher, installed_files)
+        return {file[1]: file[0] for file in files} if files else {}
+
+    @classmethod
+    def pepareDownloadFileList(cls) -> list:
+        """Prepare file list to be downloaded"""
+        LOGGER.debug("Preparing file list to be downloaded.")
+        remote_files = cls.getFiles()
+        local_files = cls.getLocalFiles()
+        download_list = []
+        for filename in remote_files.keys():
+            if filename in local_files.keys():
+                if remote_files[filename] != local_files[filename]:
+                    download_list.append(filename)
+            else:
+                download_list.append(filename)
+        return download_list
+
+    @classmethod
+    def downloadRelease(cls) -> None:
+        """Download latest RefSeq database release."""
+        files = cls.pepareDownloadFileList()
+        url = ""
+        LOGGER.timeit()
+        with ThreadPoolExecutor(max_workers=3) as executor:
+            for file in files:
+                future = executor.submit(downloadFile, url, cls.__name__, file)
+                LOGGER.info(future.result())
+        LOGGER.report()
+
+    @classmethod
+    def saveRelease(cls) -> None:
+        """Write current release version to disk."""
+        current_release = cls.getCurrentRelease()
+        path = os.path.join(PRODY_DATA, cls.__name__)
+        os.makedirs(path, exist_ok=True)
+        with open(f"{PRODY_DATA}/{cls.__name__}/{cls.RELEASE}", "w", encoding="utf-8") as file:
+            file.write(current_release)
+        LOGGER.debug("RefSeq release {} saved.".format(current_release))
+
+    @classmethod
+    def updateRelease(cls) -> None:
+        """Update release to the most recent one."""
+        LOGGER.debug("Updating RefSeq release version.")
+        cls.downloadRelease()
+        cls.saveRelease()
+
+    @classmethod
+    def getLocalRelease(cls) -> str:
+        """Get release version from local disk."""
+        LOGGER.debug("Getting RefSeq local release version.")
+        path = os.path.join(PRODY_DATA, cls.__name__)
+        os.makedirs(path, exist_ok=True)
+        with open(f"{PRODY_DATA}/{cls.__name__}/{cls.RELEASE}", "r", encoding="utf-8") as file:
+            return file.readline()
+
+    @classmethod
+    def checkForUpdates(cls) -> None:
+        """Check if local version is the recent one."""
+        LOGGER.debug("RefSeq checking for updates.")
+        if cls.getCurrentRelease() != cls.getLocalRelease():
+            cls.updateRelease()

prody/database/swissprot.py

@@ -0,0 +1,94 @@
+# -*- coding: utf-8 -*-
+
+"""Swiss-Prot database operations."""
+
+import os
+import re
+from concurrent.futures import ThreadPoolExecutor
+
+import requests
+from prody import LOGGER
+from prody.utilities.helpers import downloadFile
+from prody.utilities.pathtools import PRODY_DATA
+
+__all__ = ["SwissProt"]
+
+
+class SwissProt:
+    """Swiss-Prot database."""
+
+    RELEASE = "release.txt"
+    HEADERS = {"User-Agent": "Python pattern search agent", "Contact": "[email protected]"}
+
+    @classmethod
+    def getCurrentRelease(cls) -> str:
+        """Get current swiss-prot db release version.
+
+        Raises:
+            Exception: No release version found.
+
+        Returns:
+            str: Swiss-prot db release version.
+        """
+        sp_release = ""
+        url = "https://ftp.expasy.org/databases/swiss-prot/release/reldate.txt"
+        try:
+            response = requests.get(url, headers=cls.HEADERS)
+        except requests.exceptions.RequestException as exception:
+            LOGGER.error(str(exception))
+        else:
+            sp_release = re.search(r"Swiss-Prot Release (\d{4}_\d{2})", response.text)
+        if not sp_release:
+            LOGGER.error("Could't determine release version.")
+        LOGGER.debug("Swiss-Prot current release: {}".format(sp_release[1]))
+        return sp_release[1]
+
+    @classmethod
+    def downloadRelease(cls, types=None) -> None:
+        """Download latest swiss-prot database release.
+
+        Args:
+            types (list, optional): Database file types. Defaults to None.
+        """
+        types = types if types else ["xml", "dat", "fasta"]
+        files = [f"uniprot_sprot.{type}.gz" for type in types]
+        url = "https://ftp.expasy.org/databases/swiss-prot/release/"
+        LOGGER.timeit()
+        with ThreadPoolExecutor(max_workers=3) as executor:
+            for file in files:
+                future = executor.submit(downloadFile, url, cls.__name__, file, headers=cls.HEADERS)
+                LOGGER.info(future.result())
+        LOGGER.report()
+
+    @classmethod
+    def saveRelease(cls) -> None:
+        """Write current release version to disk."""
+        current_release = cls.getCurrentRelease()
+        path = os.path.join(PRODY_DATA, cls.__name__)
+        os.makedirs(path, exist_ok=True)
+        with open(f"{PRODY_DATA}/{cls.__name__}/{cls.RELEASE}", "w", encoding="utf-8") as file:
+            file.write(current_release)
+        LOGGER.debug("Swiss-Prot release {} saved.".format(current_release))
+
+    @classmethod
+    def updateRelease(cls) -> None:
+        """Update release to the most recent one."""
+        LOGGER.debug("Updating Swiss-Prot release version.")
+        cls.downloadRelease()
+        cls.saveRelease()
+
+    @classmethod
+    def getLocalRelease(cls) -> str:
+        """Get release version from local disk."""
+        LOGGER.debug("Getting Swiss-Prot local release version.")
+        path = os.path.join(PRODY_DATA, cls.__name__)
+        os.makedirs(path, exist_ok=True)
+        with open(f"{PRODY_DATA}/{cls.__name__}/{cls.RELEASE}", "r", encoding="utf-8") as file:
+            return file.readline()
+
+    @classmethod
+    def checkForUpdates(cls) -> None:
+        """Check if local version is the recent one."""
+        LOGGER.debug("Swiss-Prot checking for updates.")
+        if cls.getCurrentRelease() != cls.getLocalRelease():
+            cls.updateRelease()

prody/sequence/__init__.py

@@ -46,10 +46,19 @@
   * :func:`.showShannonEntropy` - plot Shannon entropy
   * :func:`.showMSAOccupancy` - plot row (sequence) or column occupancy
   * :func:`.showMutinfoMatrix` - show mutual information matrix
+
+
+Searching
+========
+  * :func:`.getPdbCodesFromMotif` - get PDB code from MOTIF
 """
 
 __all__ = []
 
+from . import motif
+from .motif import *
+__all__.extend(motif.__all__)
+
 from . import msa
 from .msa import *
 __all__.extend(msa.__all__)
@@ -69,4 +78,3 @@
 from . import sequence
 from .sequence import *
 __all__.extend(sequence.__all__)
-