File.py

# Copyright 1999 by Jeffrey Chang.  All rights reserved.
# Copyright 2009-2012 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.

StringHandle   Wraps a file object around a string.  This is now DEPRECATED,
               and is likely to be removed in a future release of Biopython.

SGMLStripper   Object that strips SGML.  This is now DEPRECATED, and is likely
               to be removed in a future release of Biopython.

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.
"""
# For with statement in Python 2.5
from __future__ import with_statement
import codecs
import os
import contextlib
import StringIO
import itertools

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()
    """
    if isinstance(handleish, basestring):
        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")
    import bgzf
    try:
        return bgzf.BgzfReader(mode="rb", fileobj=handle)
    except ValueError, 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

    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):
        lengths = map(len, self._saved)
        sum = reduce(lambda x, y: x+y, lengths, 0)
        return self._handle.tell() - sum

    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()


# I could make this faster by using cStringIO.
# However, cStringIO (in v1.52) does not implement the
# readlines method.
class StringHandle(StringIO.StringIO):
    def __init__(self, buffer=''):
        import warnings
        import Bio
        warnings.warn("This class is deprecated, and is likely to be removed in a future version of Biopython. Please use the class StringIO in the module StringIO in the Python standard library instead", Bio.BiopythonDeprecationWarning)
        StringIO.StringIO.__init__(self, buffer)

try:
    import sgmllib
except ImportError:
    #This isn't available on Python 3, but we don't care much as SGMLStripper
    #is obsolete
    pass
else:
    class SGMLStripper(object):
        """Object to strip SGML tags (OBSOLETE)."""
        class MyParser(sgmllib.SGMLParser):
            def __init__(self):
                sgmllib.SGMLParser.__init__(self)
                self.data = ''

            def handle_data(self, data):
                self.data = self.data + data

        def __init__(self):
            import warnings
            import Bio
            warnings.warn("This class is deprecated, and is likely to be removed in a future version of Biopython", Bio.BiopythonDeprecationWarning)
            self._parser = SGMLStripper.MyParser()

        def strip(self, str):
            """S.strip(str) -> string

            Strip the SGML tags from str.

            """
            if not str:  # empty string, don't do anything.
                return ''
            # I need to make sure that I don't return an empty string if
            # the buffer is not empty.  This can happen if there's a newline
            # character embedded within a tag.  Thus, I'll first check to
            # see if the last character is a newline.  If it is, and it's stripped
            # away, I'll add it back.
            is_newline = str[-1] in ['\n', '\r']

            self._parser.data = ''    # clear the parser's data (don't reset)
            self._parser.feed(str)
            if self._parser.data:
                str = self._parser.data
            elif is_newline:
                str = '\n'
            else:
                str = ''
            return str


#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(...), ...}" % (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)

    if hasattr(dict, "iteritems"):
        #Python 2, use iteritems but not items etc
        def values(self):
            """Would be a list of the SeqRecord objects, but not implemented.

            In general you can be indexing very very large files, with millions
            of sequences. Loading all these into memory at once as SeqRecord
            objects would (probably) use up all the RAM. Therefore we simply
            don't support this dictionary method.
            """
            raise NotImplementedError("Due to memory concerns, when indexing a "
                                      "sequence file you cannot access all the "
                                      "records at once.")

        def items(self):
            """Would be a list of the (key, SeqRecord) tuples, but not implemented.

            In general you can be indexing very very large files, with millions
            of sequences. Loading all these into memory at once as SeqRecord
            objects would (probably) use up all the RAM. Therefore we simply
            don't support this dictionary method.
            """
            raise NotImplementedError("Due to memory concerns, when indexing a "
                                      "sequence file you cannot access all the "
                                      "records at once.")

        def keys(self):
            """Return a list of all the keys (SeqRecord identifiers)."""
            #TODO - Stick a warning in here for large lists? Or just refuse?
            return self._offsets.keys()

        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__()

    else:
        #Python 3 - define items and values as iterators
        def items(self):
            """Iterate over the (key, SeqRecord) items."""
            for key in self.__iter__():
                yield key, self.__getitem__(key)

        def values(self):
            """Iterate over the SeqRecord items."""
            for key in self.__iter__():
                yield self.__getitem__(key)

        def keys(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.")


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, 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, 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()