# Copyright 1999 by Jeffrey Chang. All rights reserved. # Copyright 2009-2015 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): r"""Context manager to ensure we are using a handle. 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 functionality 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 = [] try: # If wrapping an online handle, this this is nice to have: self.url = handle.url except AttributeError: pass 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): """Return the raw record from the file as a bytes string (if implemented). If the key is not found, a KeyError exception is raised. This may not have been implemented for all file formats. """ # 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): """Return the raw record from the file as a bytes string. If the key is not found, a KeyError exception is raised. """ # 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): """Loads or creates an SQLite based index.""" # 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 # Cache the arguments as private variables self._index_filename = index_filename self._filenames = filenames self._format = format self._key_function = key_function self._proxy_factory = proxy_factory self._repr = repr self._max_open = max_open self._proxies = {} # Note if using SQLite :memory: trick index filename, this will # give $PWD as the relative path (which is fine). self._relative_path = os.path.abspath(os.path.dirname(index_filename)) if os.path.isfile(index_filename): self._load_index() else: self._build_index() def _load_index(self): """Called from __init__ to re-use an existing index (PRIVATE).""" index_filename = self._index_filename relative_path = self._relative_path filenames = self._filenames format = self._format proxy_factory = self._proxy_factory 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)) try: filenames_relative_to_index, = con.execute( "SELECT value FROM meta_data WHERE key=?;", ("filenames_relative_to_index",)).fetchone() filenames_relative_to_index = (filenames_relative_to_index.upper() == "TRUE") except TypeError: # Original behaviour, assume if meta_data missing filenames_relative_to_index = False self._filenames = [row[0] for row in con.execute("SELECT name FROM file_data " "ORDER BY file_number;").fetchall()] if filenames_relative_to_index: # Not implicitly relative to $PWD, explicitly relative to index file relative_path = os.path.abspath(os.path.dirname(index_filename)) tmp = [] for f in self._filenames: if os.path.isabs(f): tmp.append(f) else: # Would be stored with Unix / path separator, so convert # it to the local OS path separator here: tmp.append(os.path.join(relative_path, f.replace("/", os.path.sep))) self._filenames = tmp del tmp 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: for old, new in zip(self._filenames, filenames): # Want exact match (after making relative to the index above) if os.path.abspath(old) != os.path.abspath(new): con.close() if filenames_relative_to_index: raise ValueError("Index file has different filenames, e.g. %r != %r" % (os.path.abspath(old), os.path.abspath(new))) else: raise ValueError("Index file has different filenames " "[This is an old index where any relative paths " "were relative to the original working directory]. " "e.g. %r != %r" % (os.path.abspath(old), os.path.abspath(new))) # Filenames are equal (after imposing abspath) 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) def _build_index(self): """Called from __init__ to create a new index (PRIVATE).""" index_filename = self._index_filename relative_path = self._relative_path filenames = self._filenames format = self._format key_function = self._key_function proxy_factory = self._proxy_factory max_open = self._max_open random_access_proxies = self._proxies if not format or not filenames: raise ValueError("Filenames to index and format required to build %r" % index_filename) 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)) con.execute("INSERT INTO meta_data (key, value) VALUES (?,?);", ("filenames_relative_to_index", "True")) # 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): # Default to storing as an absolute path, f = os.path.abspath(filename) if not os.path.isabs(filename) and not os.path.isabs(index_filename): # Since user gave BOTH filename & index as relative paths, # we will store this relative to the index file even though # if it may now start ../ (meaning up a level) # Note for cross platform use (e.g. shared drive over SAMBA), # convert any Windows slash into Unix style for rel paths. f = os.path.relpath(filename, relative_path).replace(os.path.sep, "/") elif (os.path.dirname(os.path.abspath(filename)) + os.path.sep).startswith(relative_path + os.path.sep): # Since sequence file is in same directory or sub directory, # might as well make this into a relative path: f = os.path.relpath(filename, relative_path).replace(os.path.sep, "/") assert not f.startswith("../"), f # print("DEBUG - storing %r as [%r] %r" % (filename, relative_path, f)) con.execute( "INSERT INTO file_data (file_number, name) VALUES (?,?);", (i, f)) 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") 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): """Return the raw record from the file as a bytes string. If the key is not found, a KeyError exception is raised. """ # 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()