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# Copyright 1999 by Jeffrey Chang.  All rights reserved. 

# Copyright 2009-2013 by Peter Cock. All rights reserved. 

# 

# This code is part of the Biopython distribution and governed by its 

# license.  Please see the LICENSE file that should have been included 

# as part of this package. 

 

"""Code for more fancy file handles. 

 

 

Classes: 

 

UndoHandle     File object decorator with support for undo-like operations. 

 

Additional private classes used in Bio.SeqIO and Bio.SearchIO for indexing 

files are also defined under Bio.File but these are not intended for direct 

use. 

""" 

from __future__ import print_function 

 

import codecs 

import os 

import sys 

import contextlib 

import itertools 

 

from Bio._py3k import basestring 

 

try: 

    from collections import UserDict as _dict_base 

except ImportError: 

    from UserDict import DictMixin as _dict_base 

 

try: 

    from sqlite3 import dbapi2 as _sqlite 

    from sqlite3 import IntegrityError as _IntegrityError 

    from sqlite3 import OperationalError as _OperationalError 

except ImportError: 

    #Not present on Jython, but should be included in Python 2.5 

    #or later (unless compiled from source without its dependencies) 

    #Still want to offer in-memory indexing. 

    _sqlite = None 

    pass 

 

 

@contextlib.contextmanager 

def as_handle(handleish, mode='r', **kwargs): 

    """ 

    Context manager for arguments that can be passed to 

    SeqIO and AlignIO read, write, and parse methods: either file objects or strings. 

 

    When given a string, returns a file handle open to handleish with provided 

    mode which will be closed when the manager exits. 

 

    All other inputs are returned, and are *not* closed 

 

    - handleish  - Either a string or file handle 

    - mode       - Mode to open handleish (used only if handleish is a string) 

    - kwargs     - Further arguments to pass to open(...) 

 

    Example: 

 

    >>> with as_handle('seqs.fasta', 'w') as fp: 

    ...     fp.write('>test\nACGT') 

    >>> fp.closed 

    True 

 

    >>> handle = open('seqs.fasta', 'w') 

    >>> with as_handle(handle) as fp: 

    ...     fp.write('>test\nACGT') 

    >>> fp.closed 

    False 

    >>> fp.close() 

 

    Note that if the mode argument includes U (for universal new lines) 

    this will be removed under Python 3 where is is redundant and has 

    been deprecated (this happens automatically in text mode). 

    """ 

    if isinstance(handleish, basestring): 

        if sys.version_info[0] >= 3 and "U" in mode: 

            mode = mode.replace("U", "") 

        if 'encoding' in kwargs: 

            with codecs.open(handleish, mode, **kwargs) as fp: 

                yield fp 

        else: 

            with open(handleish, mode, **kwargs) as fp: 

                yield fp 

    else: 

        yield handleish 

 

def _open_for_random_access(filename): 

    """Open a file in binary mode, spot if it is BGZF format etc (PRIVATE). 

 

    This funcationality is used by the Bio.SeqIO and Bio.SearchIO index 

    and index_db functions. 

    """ 

    handle = open(filename, "rb") 

    from . import bgzf 

    try: 

        return bgzf.BgzfReader(mode="rb", fileobj=handle) 

    except ValueError as e: 

        assert "BGZF" in str(e) 

        #Not a BGZF file after all, rewind to start: 

        handle.seek(0) 

    return handle 

 

 

class UndoHandle(object): 

    """A Python handle that adds functionality for saving lines. 

 

    Saves lines in a LIFO fashion. 

 

    Added methods: 

    saveline    Save a line to be returned next time. 

    peekline    Peek at the next line without consuming it. 

 

    """ 

    def __init__(self, handle): 

        self._handle = handle 

        self._saved = [] 

 

    def __iter__(self): 

        return self 

 

    def __next__(self): 

        next = self.readline() 

        if not next: 

            raise StopIteration 

        return next 

 

    if sys.version_info[0] < 3: 

        def next(self): 

            """Python 2 style alias for Python 3 style __next__ method.""" 

            return self.__next__() 

 

    def readlines(self, *args, **keywds): 

        lines = self._saved + self._handle.readlines(*args, **keywds) 

        self._saved = [] 

        return lines 

 

    def readline(self, *args, **keywds): 

        if self._saved: 

            line = self._saved.pop(0) 

        else: 

            line = self._handle.readline(*args, **keywds) 

        return line 

 

    def read(self, size=-1): 

        if size == -1: 

            saved = "".join(self._saved) 

            self._saved[:] = [] 

        else: 

            saved = '' 

            while size > 0 and self._saved: 

                if len(self._saved[0]) <= size: 

                    size = size - len(self._saved[0]) 

                    saved = saved + self._saved.pop(0) 

                else: 

                    saved = saved + self._saved[0][:size] 

                    self._saved[0] = self._saved[0][size:] 

                    size = 0 

        return saved + self._handle.read(size) 

 

    def saveline(self, line): 

        if line: 

            self._saved = [line] + self._saved 

 

    def peekline(self): 

        if self._saved: 

            line = self._saved[0] 

        else: 

            line = self._handle.readline() 

            self.saveline(line) 

        return line 

 

    def tell(self): 

        return self._handle.tell() - sum(len(line) for line in self._saved) 

 

    def seek(self, *args): 

        self._saved = [] 

        self._handle.seek(*args) 

 

    def __getattr__(self, attr): 

        return getattr(self._handle, attr) 

 

    def __enter__(self): 

        return self 

 

    def __exit__(self, type, value, traceback): 

        self._handle.close() 

 

 

#The rest of this file defines code used in Bio.SeqIO and Bio.SearchIO 

#for indexing 

 

class _IndexedSeqFileProxy(object): 

    """Base class for file format specific random access (PRIVATE). 

 

    This is subclasses in both Bio.SeqIO for indexing as SeqRecord 

    objects, and in Bio.SearchIO for indexing QueryResult objects. 

 

    Subclasses for each file format should define '__iter__', 'get' 

    and optionally 'get_raw' methods. 

    """ 

 

    def __iter__(self): 

        """Returns (identifier, offset, length in bytes) tuples. 

 

        The length can be zero where it is not implemented or not 

        possible for a particular file format. 

        """ 

        raise NotImplementedError("Subclass should implement this") 

 

    def get(self, offset): 

        """Returns parsed object for this entry.""" 

        #Most file formats with self contained records can be handled by 

        #parsing StringIO(_bytes_to_string(self.get_raw(offset))) 

        raise NotImplementedError("Subclass should implement this") 

 

    def get_raw(self, offset): 

        """Returns bytes string (if implemented for this file format).""" 

        #Should be done by each sub-class (if possible) 

        raise NotImplementedError("Not available for this file format.") 

 

 

class _IndexedSeqFileDict(_dict_base): 

    """Read only dictionary interface to a sequential record file. 

 

    This code is used in both Bio.SeqIO for indexing as SeqRecord 

    objects, and in Bio.SearchIO for indexing QueryResult objects. 

 

    Keeps the keys and associated file offsets in memory, reads the file 

    to access entries as objects parsing them on demand. This approach 

    is memory limited, but will work even with millions of records. 

 

    Note duplicate keys are not allowed. If this happens, a ValueError 

    exception is raised. 

 

    As used in Bio.SeqIO, by default the SeqRecord's id string is used 

    as the dictionary key. In Bio.SearchIO, the query's id string is 

    used. This can be changed by suppling an optional key_function, 

    a callback function which will be given the record id and must 

    return the desired key. For example, this allows you to parse 

    NCBI style FASTA identifiers, and extract the GI number to use 

    as the dictionary key. 

 

    Note that this dictionary is essentially read only. You cannot 

    add or change values, pop values, nor clear the dictionary. 

    """ 

    def __init__(self, random_access_proxy, key_function, 

                 repr, obj_repr): 

        #Use key_function=None for default value 

        self._proxy = random_access_proxy 

        self._key_function = key_function 

        self._repr = repr 

        self._obj_repr = obj_repr 

        if key_function: 

            offset_iter = ( 

                (key_function(k), o, l) for (k, o, l) in random_access_proxy) 

        else: 

            offset_iter = random_access_proxy 

        offsets = {} 

        for key, offset, length in offset_iter: 

            #Note - we don't store the length because I want to minimise the 

            #memory requirements. With the SQLite backend the length is kept 

            #and is used to speed up the get_raw method (by about 3 times). 

            #The length should be provided by all the current backends except 

            #SFF where there is an existing Roche index we can reuse (very fast 

            #but lacks the record lengths) 

            #assert length or format in ["sff", "sff-trim"], \ 

            #       "%s at offset %i given length %r (%s format %s)" \ 

            #       % (key, offset, length, filename, format) 

            if key in offsets: 

                self._proxy._handle.close() 

                raise ValueError("Duplicate key '%s'" % key) 

            else: 

                offsets[key] = offset 

        self._offsets = offsets 

 

    def __repr__(self): 

        return self._repr 

 

    def __str__(self): 

        #TODO - How best to handle the __str__ for SeqIO and SearchIO? 

        if self: 

            return "{%r : %s(...), ...}" % (list(self.keys())[0], self._obj_repr) 

        else: 

            return "{}" 

 

    def __contains__(self, key): 

        return key in self._offsets 

 

    def __len__(self): 

        """How many records are there?""" 

        return len(self._offsets) 

 

    def items(self): 

        """Iterate over the (key, SeqRecord) items. 

 

        This tries to act like a Python 3 dictionary, and does not return 

        a list of (key, value) pairs due to memory concerns. 

        """ 

        for key in self.__iter__(): 

            yield key, self.__getitem__(key) 

 

    def values(self): 

        """Iterate over the SeqRecord items. 

 

        This tries to act like a Python 3 dictionary, and does not return 

        a list of value due to memory concerns. 

        """ 

        for key in self.__iter__(): 

            yield self.__getitem__(key) 

 

    def keys(self): 

        """Iterate over the keys. 

 

        This tries to act like a Python 3 dictionary, and does not return 

        a list of keys due to memory concerns. 

        """ 

        return self.__iter__() 

 

    if hasattr(dict, "iteritems"): 

        #Python 2, also define iteritems etc 

        def itervalues(self): 

            """Iterate over the SeqRecord) items.""" 

            for key in self.__iter__(): 

                yield self.__getitem__(key) 

 

        def iteritems(self): 

            """Iterate over the (key, SeqRecord) items.""" 

            for key in self.__iter__(): 

                yield key, self.__getitem__(key) 

 

        def iterkeys(self): 

            """Iterate over the keys.""" 

            return self.__iter__() 

 

    def __iter__(self): 

        """Iterate over the keys.""" 

        return iter(self._offsets) 

 

    def __getitem__(self, key): 

        """x.__getitem__(y) <==> x[y]""" 

        #Pass the offset to the proxy 

        record = self._proxy.get(self._offsets[key]) 

        if self._key_function: 

            key2 = self._key_function(record.id) 

        else: 

            key2 = record.id 

        if key != key2: 

            raise ValueError("Key did not match (%s vs %s)" % (key, key2)) 

        return record 

 

    def get(self, k, d=None): 

        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None.""" 

        try: 

            return self.__getitem__(k) 

        except KeyError: 

            return d 

 

    def get_raw(self, key): 

        """Similar to the get method, but returns the record as a raw string. 

 

        If the key is not found, a KeyError exception is raised. 

 

        Note that on Python 3 a bytes string is returned, not a typical 

        unicode string. 

 

        NOTE - This functionality is not supported for every file format. 

        """ 

        #Pass the offset to the proxy 

        return self._proxy.get_raw(self._offsets[key]) 

 

    def __setitem__(self, key, value): 

        """Would allow setting or replacing records, but not implemented.""" 

        raise NotImplementedError("An indexed a sequence file is read only.") 

 

    def update(self, *args, **kwargs): 

        """Would allow adding more values, but not implemented.""" 

        raise NotImplementedError("An indexed a sequence file is read only.") 

 

    def pop(self, key, default=None): 

        """Would remove specified record, but not implemented.""" 

        raise NotImplementedError("An indexed a sequence file is read only.") 

 

    def popitem(self): 

        """Would remove and return a SeqRecord, but not implemented.""" 

        raise NotImplementedError("An indexed a sequence file is read only.") 

 

    def clear(self): 

        """Would clear dictionary, but not implemented.""" 

        raise NotImplementedError("An indexed a sequence file is read only.") 

 

    def fromkeys(self, keys, value=None): 

        """A dictionary method which we don't implement.""" 

        raise NotImplementedError("An indexed a sequence file doesn't " 

                                  "support this.") 

 

    def copy(self): 

        """A dictionary method which we don't implement.""" 

        raise NotImplementedError("An indexed a sequence file doesn't " 

                                  "support this.") 

 

    def close(self): 

        """Close the file handle being used to read the data. 

 

        Once called, further use of the index won't work. The sole purpose 

        of this method is to allow explicit handle closure - for example 

        if you wish to delete the file, on Windows you must first close 

        all open handles to that file. 

        """ 

        self._proxy._handle.close() 

 

 

class _SQLiteManySeqFilesDict(_IndexedSeqFileDict): 

    """Read only dictionary interface to many sequential record files. 

 

    This code is used in both Bio.SeqIO for indexing as SeqRecord 

    objects, and in Bio.SearchIO for indexing QueryResult objects. 

 

    Keeps the keys, file-numbers and offsets in an SQLite database. To access 

    a record by key, reads from the offset in the appropriate file and then 

    parses the record into an object. 

 

    There are OS limits on the number of files that can be open at once, 

    so a pool are kept. If a record is required from a closed file, then 

    one of the open handles is closed first. 

    """ 

    def __init__(self, index_filename, filenames, 

                 proxy_factory, format, 

                 key_function, repr, max_open=10): 

        self._proxy_factory = proxy_factory 

        self._repr = repr 

        random_access_proxies = {} 

        #TODO? - Don't keep filename list in memory (just in DB)? 

        #Should save a chunk of memory if dealing with 1000s of files. 

        #Furthermore could compare a generator to the DB on reloading 

        #(no need to turn it into a list) 

        if not _sqlite: 

            # Hack for Jython (of if Python is compiled without it) 

            from Bio import MissingPythonDependencyError 

            raise MissingPythonDependencyError("Requires sqlite3, which is " 

                                               "included Python 2.5+") 

        if filenames is not None: 

            filenames = list(filenames)  # In case it was a generator 

        if os.path.isfile(index_filename): 

            #Reuse the index. 

            con = _sqlite.connect(index_filename) 

            self._con = con 

            #Check the count... 

            try: 

                count, = con.execute( 

                    "SELECT value FROM meta_data WHERE key=?;", 

                    ("count",)).fetchone() 

                self._length = int(count) 

                if self._length == -1: 

                    con.close() 

                    raise ValueError("Unfinished/partial database") 

                count, = con.execute( 

                    "SELECT COUNT(key) FROM offset_data;").fetchone() 

                if self._length != int(count): 

                    con.close() 

                    raise ValueError("Corrupt database? %i entries not %i" 

                                     % (int(count), self._length)) 

                self._format, = con.execute( 

                    "SELECT value FROM meta_data WHERE key=?;", 

                                           ("format",)).fetchone() 

                if format and format != self._format: 

                    con.close() 

                    raise ValueError("Index file says format %s, not %s" 

                                     % (self._format, format)) 

                self._filenames = [row[0] for row in 

                                   con.execute("SELECT name FROM file_data " 

                                               "ORDER BY file_number;").fetchall()] 

                if filenames and len(filenames) != len(self._filenames): 

                    con.close() 

                    raise ValueError("Index file says %i files, not %i" 

                                     % (len(self._filenames), len(filenames))) 

                if filenames and filenames != self._filenames: 

                    con.close() 

                    raise ValueError("Index file has different filenames") 

            except _OperationalError as err: 

                con.close() 

                raise ValueError("Not a Biopython index database? %s" % err) 

            #Now we have the format (from the DB if not given to us), 

            if not proxy_factory(self._format): 

                con.close() 

                raise ValueError("Unsupported format '%s'" % self._format) 

        else: 

            self._filenames = filenames 

            self._format = format 

            if not format or not filenames: 

                raise ValueError("Filenames to index and format required") 

            if not proxy_factory(format): 

                raise ValueError("Unsupported format '%s'" % format) 

            #Create the index 

            con = _sqlite.connect(index_filename) 

            self._con = con 

            #print("Creating index") 

            # Sqlite PRAGMA settings for speed 

            con.execute("PRAGMA synchronous=OFF") 

            con.execute("PRAGMA locking_mode=EXCLUSIVE") 

            #Don't index the key column until the end (faster) 

            #con.execute("CREATE TABLE offset_data (key TEXT PRIMARY KEY, " 

            # "offset INTEGER);") 

            con.execute("CREATE TABLE meta_data (key TEXT, value TEXT);") 

            con.execute("INSERT INTO meta_data (key, value) VALUES (?,?);", 

                        ("count", -1)) 

            con.execute("INSERT INTO meta_data (key, value) VALUES (?,?);", 

                        ("format", format)) 

            #TODO - Record the alphabet? 

            #TODO - Record the file size and modified date? 

            con.execute( 

                "CREATE TABLE file_data (file_number INTEGER, name TEXT);") 

            con.execute("CREATE TABLE offset_data (key TEXT, file_number INTEGER, offset INTEGER, length INTEGER);") 

            count = 0 

            for i, filename in enumerate(filenames): 

                con.execute( 

                    "INSERT INTO file_data (file_number, name) VALUES (?,?);", 

                    (i, filename)) 

                random_access_proxy = proxy_factory(format, filename) 

                if key_function: 

                    offset_iter = ((key_function( 

                        k), i, o, l) for (k, o, l) in random_access_proxy) 

                else: 

                    offset_iter = ( 

                        (k, i, o, l) for (k, o, l) in random_access_proxy) 

                while True: 

                    batch = list(itertools.islice(offset_iter, 100)) 

                    if not batch: 

                        break 

                    #print("Inserting batch of %i offsets, %s ... %s" \ 

                    # % (len(batch), batch[0][0], batch[-1][0])) 

                    con.executemany( 

                        "INSERT INTO offset_data (key,file_number,offset,length) VALUES (?,?,?,?);", 

                        batch) 

                    con.commit() 

                    count += len(batch) 

                if len(random_access_proxies) < max_open: 

                    random_access_proxies[i] = random_access_proxy 

                else: 

                    random_access_proxy._handle.close() 

            self._length = count 

            #print("About to index %i entries" % count) 

            try: 

                con.execute("CREATE UNIQUE INDEX IF NOT EXISTS " 

                            "key_index ON offset_data(key);") 

            except _IntegrityError as err: 

                self._proxies = random_access_proxies 

                self.close() 

                con.close() 

                raise ValueError("Duplicate key? %s" % err) 

            con.execute("PRAGMA locking_mode=NORMAL") 

            con.execute("UPDATE meta_data SET value = ? WHERE key = ?;", 

                        (count, "count")) 

            con.commit() 

            #print("Index created") 

        self._proxies = random_access_proxies 

        self._max_open = max_open 

        self._index_filename = index_filename 

        self._key_function = key_function 

 

    def __repr__(self): 

        return self._repr 

 

    def __contains__(self, key): 

        return bool( 

            self._con.execute("SELECT key FROM offset_data WHERE key=?;", 

                   (key,)).fetchone()) 

 

    def __len__(self): 

        """How many records are there?""" 

        return self._length 

        #return self._con.execute("SELECT COUNT(key) FROM offset_data;").fetchone()[0] 

 

    def __iter__(self): 

        """Iterate over the keys.""" 

        for row in self._con.execute("SELECT key FROM offset_data;"): 

            yield str(row[0]) 

 

    if hasattr(dict, "iteritems"): 

        #Python 2, use iteritems but not items etc 

        #Just need to override this... 

        def keys(self): 

            """Return a list of all the keys (SeqRecord identifiers).""" 

            return [str(row[0]) for row in 

                    self._con.execute("SELECT key FROM offset_data;").fetchall()] 

 

    def __getitem__(self, key): 

        """x.__getitem__(y) <==> x[y]""" 

        #Pass the offset to the proxy 

        row = self._con.execute( 

            "SELECT file_number, offset FROM offset_data WHERE key=?;", 

            (key,)).fetchone() 

        if not row: 

            raise KeyError 

        file_number, offset = row 

        proxies = self._proxies 

        if file_number in proxies: 

            record = proxies[file_number].get(offset) 

        else: 

            if len(proxies) >= self._max_open: 

                #Close an old handle... 

                proxies.popitem()[1]._handle.close() 

            #Open a new handle... 

            proxy = self._proxy_factory(self._format, self._filenames[file_number]) 

            record = proxy.get(offset) 

            proxies[file_number] = proxy 

        if self._key_function: 

            key2 = self._key_function(record.id) 

        else: 

            key2 = record.id 

        if key != key2: 

            raise ValueError("Key did not match (%s vs %s)" % (key, key2)) 

        return record 

 

    def get(self, k, d=None): 

        """D.get(k[,d]) -> D[k] if k in D, else d.  d defaults to None.""" 

        try: 

            return self.__getitem__(k) 

        except KeyError: 

            return d 

 

    def get_raw(self, key): 

        """Similar to the get method, but returns the record as a raw string. 

 

        If the key is not found, a KeyError exception is raised. 

 

        Note that on Python 3 a bytes string is returned, not a typical 

        unicode string. 

 

        NOTE - This functionality is not supported for every file format. 

        """ 

        #Pass the offset to the proxy 

        row = self._con.execute( 

            "SELECT file_number, offset, length FROM offset_data WHERE key=?;", 

            (key,)).fetchone() 

        if not row: 

            raise KeyError 

        file_number, offset, length = row 

        proxies = self._proxies 

        if file_number in proxies: 

            if length: 

                #Shortcut if we have the length 

                h = proxies[file_number]._handle 

                h.seek(offset) 

                return h.read(length) 

            else: 

                return proxies[file_number].get_raw(offset) 

        else: 

            #This code is duplicated from __getitem__ to avoid a function call 

            if len(proxies) >= self._max_open: 

                #Close an old handle... 

                proxies.popitem()[1]._handle.close() 

            #Open a new handle... 

            proxy = self._proxy_factory(self._format, self._filenames[file_number]) 

            proxies[file_number] = proxy 

            if length: 

                #Shortcut if we have the length 

                h = proxy._handle 

                h.seek(offset) 

                return h.read(length) 

            else: 

                return proxy.get_raw(offset) 

 

    def close(self): 

        """Close any open file handles.""" 

        proxies = self._proxies 

        while proxies: 

            proxies.popitem()[1]._handle.close()