# Copyright 2009-2011 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.
"""Dictionary like indexing of sequence files (PRIVATE).
You are not expected to access this module, or any of its code, directly. This
is all handled internally by the Bio.SeqIO.index(...) function which is the
public interface for this functionality.
The basic idea is that we scan over a sequence file, looking for new record
markers. We then try and extract the string that Bio.SeqIO.parse/read would
use as the record id, ideally without actually parsing the full record. We
then use a subclassed Python dictionary to record the file offset for the
record start against the record id.
Note that this means full parsing is on demand, so any invalid or problem
record may not trigger an exception until it is accessed. This is by design.
This means our dictionary like objects have in memory ALL the keys (all the
record identifiers), which shouldn't be a problem even with second generation
sequencing. If this is an issue later on, storing the keys and offsets in a
temp lookup file might be one idea (e.g. using SQLite or an OBDA style index).
"""
import os
try:
from collections import UserDict as _dict_base
except ImportError:
from UserDict import DictMixin as _dict_base
import re
import itertools
from StringIO import StringIO
try:
from sqlite3 import dbapi2 as _sqlite
from sqlite3 import IntegrityError as _IntegrityError
from sqlite3 import OperationalError as _OperationalError
except ImportError:
#Not expected to be present on Python 2.4, ignore it
#and at least offer Bio.SeqIO.index() functionality
_sqlite = None
pass
from Bio._py3k import _bytes_to_string, _as_bytes, _as_string
from Bio import SeqIO
from Bio import Alphabet
class _IndexedSeqFileDict(_dict_base):
"""Read only dictionary interface to a sequential sequence file.
Keeps the keys and associated file offsets in memory, reads the file to
access entries as SeqRecord objects using Bio.SeqIO for parsing them.
This approach is memory limited, but will work even with millions of
sequences.
Note - as with the Bio.SeqIO.to_dict() function, duplicate keys
(record identifiers by default) are not allowed. If this happens,
a ValueError exception is raised.
By default the SeqRecord's id string is used as the dictionary
key. 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, filename, format, alphabet, key_function):
#Use key_function=None for default value
try:
proxy_class = _FormatToRandomAccess[format]
except KeyError:
raise ValueError("Unsupported format '%s'" % format)
random_access_proxy = proxy_class(filename, format, alphabet)
self._proxy = random_access_proxy
self._key_function = key_function
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).
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 "SeqIO.index(%r, %r, alphabet=%r, key_function=%r)" \
% (self._proxy._handle.name, self._proxy._format,
self._proxy._alphabet, self._key_function)
def __str__(self):
if self:
return "{%s : SeqRecord(...), ...}" % repr(self.keys()[0])
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 sequence files.
Keeps the keys, file-numbers and offsets in an SQLite database. To access
a record by key, reads from the offset in the approapriate file using
Bio.SeqIO for parsing.
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, format, alphabet,
key_function, max_open=10):
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 Python 2.4 (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),
try:
proxy_class = _FormatToRandomAccess[self._format]
except KeyError:
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")
try:
proxy_class = _FormatToRandomAccess[format]
except KeyError:
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_class(filename, format, alphabet)
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._alphabet = alphabet
self._key_function = key_function
def __repr__(self):
return "SeqIO.index_db(%r, filenames=%r, format=%r, alphabet=%r, key_function=%r)" \
% (self._index_filename, self._filenames, self._format,
self._alphabet, self._key_function)
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 = _FormatToRandomAccess[self._format]( \
self._filenames[file_number],
self._format, self._alphabet)
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 = _FormatToRandomAccess[self._format]( \
self._filenames[file_number],
self._format, self._alphabet)
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()
##############################################################################
class SeqFileRandomAccess(object):
def __init__(self, filename, format, alphabet):
self._handle = open(filename, "rb")
self._alphabet = alphabet
self._format = format
#Load the parser class/function once an avoid the dict lookup in each
#__getitem__ call:
i = SeqIO._FormatToIterator[format]
#The following alphabet code is a bit nasty... duplicates logic in
#Bio.SeqIO.parse()
if alphabet is None:
def _parse(handle):
"""Dynamically generated parser function (PRIVATE)."""
return i(handle).next()
else:
#TODO - Detect alphabet support ONCE at __init__
def _parse(handle):
"""Dynamically generated parser function (PRIVATE)."""
try:
return i(handle, alphabet=alphabet).next()
except TypeError:
return SeqIO._force_alphabet(i(handle),
alphabet).next()
self._parse = _parse
def __iter__(self):
"""Returns (id,offset) tuples."""
raise NotImplementedError("Subclass should implement this")
def get(self, offset):
"""Returns SeqRecord."""
#Should be overriden for binary file formats etc:
return self._parse(StringIO(_bytes_to_string(self.get_raw(offset))))
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.")
####################
# Special indexers #
####################
# Anything where the records cannot be read simply by parsing from
# the record start. For example, anything requiring information from
# a file header - e.g. SFF files where we would need to know the
# number of flows.
class SffRandomAccess(SeqFileRandomAccess):
"""Random access to a Standard Flowgram Format (SFF) file."""
def __init__(self, filename, format, alphabet):
SeqFileRandomAccess.__init__(self, filename, format, alphabet)
header_length, index_offset, index_length, number_of_reads, \
self._flows_per_read, self._flow_chars, self._key_sequence \
= SeqIO.SffIO._sff_file_header(self._handle)
def __iter__(self):
"""Load any index block in the file, or build it the slow way (PRIVATE)."""
if self._alphabet is None:
self._alphabet = Alphabet.generic_dna
handle = self._handle
handle.seek(0)
#Alread did this in __init__ but need handle in right place
header_length, index_offset, index_length, number_of_reads, \
self._flows_per_read, self._flow_chars, self._key_sequence \
= SeqIO.SffIO._sff_file_header(handle)
if index_offset and index_length:
#There is an index provided, try this the fast way:
count = 0
try :
for name, offset in SeqIO.SffIO._sff_read_roche_index(handle) :
yield name, offset, 0
count += 1
assert count == number_of_reads, \
"Indexed %i records, expected %i" \
% (count, number_of_reads)
return
except ValueError, err :
import warnings
warnings.warn("Could not parse the SFF index: %s" % err)
assert count==0, "Partially populated index"
handle.seek(0)
#We used to give a warning in this case, but Ion Torrent's
#SFF files don't have an index so that would be annoying.
#Fall back on the slow way!
count = 0
for name, offset in SeqIO.SffIO._sff_do_slow_index(handle) :
yield name, offset, 0
count += 1
assert count == number_of_reads, \
"Indexed %i records, expected %i" % (count, number_of_reads)
def get(self, offset) :
handle = self._handle
handle.seek(offset)
return SeqIO.SffIO._sff_read_seq_record(handle,
self._flows_per_read,
self._flow_chars,
self._key_sequence,
self._alphabet)
def get_raw(self, offset):
handle = self._handle
handle.seek(offset)
return SeqIO.SffIO._sff_read_raw_record(handle, self._flows_per_read)
class SffTrimedRandomAccess(SffRandomAccess) :
def get(self, offset) :
handle = self._handle
handle.seek(offset)
return SeqIO.SffIO._sff_read_seq_record(handle,
self._flows_per_read,
self._flow_chars,
self._key_sequence,
self._alphabet,
trim=True)
###################
# Simple indexers #
###################
class SequentialSeqFileRandomAccess(SeqFileRandomAccess):
def __init__(self, filename, format, alphabet):
SeqFileRandomAccess.__init__(self, filename, format, alphabet)
marker = {"ace" : "CO ",
"embl" : "ID ",
"fasta" : ">",
"genbank" : "LOCUS ",
"gb": "LOCUS ",
"imgt" : "ID ",
"phd" : "BEGIN_SEQUENCE",
"pir" : ">..;",
"qual": ">",
"qual": ">",
"swiss" : "ID ",
"uniprot-xml" : " end of this record
break
lines.append(line)
return _as_bytes("").join(lines)
#######################################
# Fiddly indexers: GenBank, EMBL, ... #
#######################################
class GenBankRandomAccess(SequentialSeqFileRandomAccess):
"""Indexed dictionary like access to a GenBank file."""
def __iter__(self):
handle = self._handle
handle.seek(0)
marker_re = self._marker_re
dot_char = _as_bytes(".")
accession_marker = _as_bytes("ACCESSION ")
version_marker = _as_bytes("VERSION ")
#Skip and header before first record
while True:
start_offset = handle.tell()
line = handle.readline()
if marker_re.match(line) or not line:
break
#Should now be at the start of a record, or end of the file
while marker_re.match(line):
#We cannot assume the record.id is the first word after LOCUS,
#normally the first entry on the VERSION or ACCESSION line is used.
key = None
while True:
line = handle.readline()
if marker_re.match(line) or not line:
if not key:
raise ValueError("Did not find ACCESSION/VERSION lines")
end_offset = handle.tell() - len(line)
yield _bytes_to_string(key), start_offset, end_offset - start_offset
start_offset = end_offset
break
elif line.startswith(accession_marker):
key = line.rstrip().split()[1]
elif line.startswith(version_marker):
version_id = line.rstrip().split()[1]
if version_id.count(dot_char)==1 and version_id.split(dot_char)[1].isdigit():
#This should mimic the GenBank parser...
key = version_id
assert not line, repr(line)
class EmblRandomAccess(SequentialSeqFileRandomAccess):
"""Indexed dictionary like access to an EMBL file."""
def __iter__(self):
handle = self._handle
handle.seek(0)
marker_re = self._marker_re
semi_char = _as_bytes(";")
dot_char = _as_bytes(".")
sv_marker = _as_bytes("SV ")
#Skip any header before first record
while True:
start_offset = handle.tell()
line = handle.readline()
if marker_re.match(line) or not line:
break
#Should now be at the start of a record, or end of the file
while marker_re.match(line):
#We cannot assume the record.id is the first word after ID,
#normally the SV line is used.
if line[2:].count(semi_char) == 6:
#Looks like the semi colon separated style introduced in 2006
parts = line[3:].rstrip().split(semi_char)
if parts[1].strip().startswith(sv_marker):
#The SV bit gives the version
key = parts[0].strip() + dot_char + parts[1].strip().split()[1]
else:
key = parts[0].strip()
elif line[2:].count(semi_char) == 3:
#Looks like the pre 2006 style, take first word only
key = line[3:].strip().split(None,1)[0]
else:
raise ValueError('Did not recognise the ID line layout:\n' + line)
while True:
line = handle.readline()
if marker_re.match(line) or not line:
end_offset = handle.tell() - len(line)
yield _bytes_to_string(key), start_offset, end_offset - start_offset
start_offset = end_offset
break
elif line.startswith(sv_marker):
key = line.rstrip().split()[1]
assert not line, repr(line)
class SwissRandomAccess(SequentialSeqFileRandomAccess):
"""Random access to a SwissProt file."""
def __iter__(self):
handle = self._handle
handle.seek(0)
marker_re = self._marker_re
semi_char = _as_bytes(";")
#Skip any header before first record
while True:
start_offset = handle.tell()
line = handle.readline()
if marker_re.match(line) or not line:
break
#Should now be at the start of a record, or end of the file
while marker_re.match(line):
#We cannot assume the record.id is the first word after ID,
#normally the following AC line is used.
line = handle.readline()
assert line.startswith(_as_bytes("AC "))
key = line[3:].strip().split(semi_char)[0].strip()
while True:
line = handle.readline()
if marker_re.match(line) or not line:
end_offset = handle.tell() - len(line)
yield _bytes_to_string(key), start_offset, end_offset - start_offset
start_offset = end_offset
break
assert not line, repr(line)
class UniprotRandomAccess(SequentialSeqFileRandomAccess):
"""Random access to a UniProt XML file."""
def __iter__(self):
handle = self._handle
handle.seek(0)
marker_re = self._marker_re
start_acc_marker = _as_bytes("")
end_acc_marker = _as_bytes("")
end_entry_marker = _as_bytes("")
#Skip any header before first record
while True:
start_offset = handle.tell()
line = handle.readline()
if marker_re.match(line) or not line:
break
#Should now be at the start of a record, or end of the file
while marker_re.match(line):
#We expect the next line to be xxx
#(possibly with leading spaces)
#but allow it to be later on within the
key = None
done = False
while True:
line = handle.readline()
if key is None and start_acc_marker in line:
assert end_acc_marker in line, line
key = line[line.find(start_acc_marker)+11:].split(_as_bytes("<"))[0]
elif end_entry_marker in line:
end_offset = handle.tell() - len(line) \
+ line.find(end_entry_marker) + 8
break
elif marker_re.match(line) or not line:
#Start of next record or end of file
raise ValueError("Didn't find end of record")
if not key:
raise ValueError("Did not find line in bytes %i to %i" \
% (start_offset, end_offset))
yield _bytes_to_string(key), start_offset, end_offset - start_offset
#Find start of next record
while not marker_re.match(line) and line:
start_offset = handle.tell()
line = handle.readline()
assert not line, repr(line)
def get_raw(self, offset):
"""Similar to the get method, but returns the record as a raw string."""
handle = self._handle
marker_re = self._marker_re
end_entry_marker = _as_bytes("")
handle.seek(offset)
data = handle.readline()
while True:
line = handle.readline()
i = line.find(end_entry_marker)
if i != -1:
data += line[:i+8]
break
if marker_re.match(line) or not line:
#End of file, or start of next record
raise ValueError("Didn't find end of record")
data += line
return data
def get(self, offset) :
#TODO - Can we handle this directly in the parser?
#This is a hack - use get_raw for ... and wrap it with
#the apparently required XML header and footer.
data = """
%s
""" % _bytes_to_string(self.get_raw(offset))
#TODO - For consistency, this function should not accept a string:
return SeqIO.UniprotIO.UniprotIterator(data).next()
class IntelliGeneticsRandomAccess(SeqFileRandomAccess):
"""Random access to a IntelliGenetics file."""
def __init__(self, filename, format, alphabet):
SeqFileRandomAccess.__init__(self, filename, format, alphabet)
self._marker_re = re.compile(_as_bytes("^;"))
def __iter__(self):
handle = self._handle
handle.seek(0)
marker_re = self._marker_re
semi_char = _as_bytes(";")
while True:
offset = handle.tell()
line = handle.readline()
if marker_re.match(line):
#Now look for the first line which doesn't start ";"
while True:
line = handle.readline()
if line[0:1] != semi_char and line.strip():
key = line.split()[0]
yield _bytes_to_string(key), offset, 0
break
if not line:
raise ValueError("Premature end of file?")
elif not line:
#End of file
break
def get_raw(self, offset):
handle = self._handle
handle.seek(offset)
marker_re = self._marker_re
lines = []
line = handle.readline()
semi_char = _as_bytes(";")
while line.startswith(semi_char):
lines.append(line)
line = handle.readline()
while line and not line.startswith(semi_char):
lines.append(line)
line = handle.readline()
return _as_bytes("").join(lines)
class TabRandomAccess(SeqFileRandomAccess):
"""Random access to a simple tabbed file."""
def __iter__(self):
handle = self._handle
handle.seek(0)
start_offset = handle.tell()
tab_char = _as_bytes("\t")
while True:
line = handle.readline()
if not line : break #End of file
try:
key = line.split(tab_char)[0]
except ValueError, err:
if not line.strip():
#Ignore blank lines
start_offset = handle.tell()
continue
else:
raise err
else:
end_offset = handle.tell()
yield _bytes_to_string(key), start_offset, end_offset - start_offset
start_offset = end_offset
def get_raw(self, offset):
"""Like the get method, but returns the record as a raw string."""
handle = self._handle
handle.seek(offset)
return handle.readline()
##########################
# Now the FASTQ indexers #
##########################
class FastqRandomAccess(SeqFileRandomAccess):
"""Random access to a FASTQ file (any supported variant).
With FASTQ the records all start with a "@" line, but so can quality lines.
Note this will cope with line-wrapped FASTQ files.
"""
def __iter__(self):
handle = self._handle
handle.seek(0)
id = None
start_offset = handle.tell()
line = handle.readline()
if not line:
#Empty file!
return
at_char = _as_bytes("@")
plus_char = _as_bytes("+")
if line[0:1] != at_char:
raise ValueError("Problem with FASTQ @ line:\n%s" % repr(line))
while line:
#assert line[0]=="@"
#This record seems OK (so far)
id = line[1:].rstrip().split(None, 1)[0]
#Find the seq line(s)
seq_len = 0
while line:
line = handle.readline()
if line.startswith(plus_char) : break
seq_len += len(line.strip())
if not line:
raise ValueError("Premature end of file in seq section")
#assert line[0]=="+"
#Find the qual line(s)
qual_len = 0
while line:
if seq_len == qual_len:
#Should be end of record...
line = handle.readline()
if line and line[0:1] != at_char:
ValueError("Problem with line %s" % repr(line))
break
else:
line = handle.readline()
qual_len += len(line.strip())
if seq_len != qual_len:
raise ValueError("Problem with quality section")
end_offset = handle.tell() - len(line)
yield _bytes_to_string(id), start_offset, end_offset - start_offset
start_offset = end_offset
#print "EOF"
def get_raw(self, offset):
"""Similar to the get method, but returns the record as a raw string."""
#TODO - Refactor this and the __init__ method to reduce code duplication?
handle = self._handle
handle.seek(offset)
line = handle.readline()
data = line
at_char = _as_bytes("@")
plus_char = _as_bytes("+")
if line[0:1] != at_char:
raise ValueError("Problem with FASTQ @ line:\n%s" % repr(line))
identifier = line[1:].rstrip().split(None, 1)[0]
#Find the seq line(s)
seq_len = 0
while line:
line = handle.readline()
data += line
if line.startswith(plus_char) : break
seq_len += len(line.strip())
if not line:
raise ValueError("Premature end of file in seq section")
assert line[0:1] == plus_char
#Find the qual line(s)
qual_len = 0
while line:
if seq_len == qual_len:
#Should be end of record...
pos = handle.tell()
line = handle.readline()
if line and line[0:1] != at_char:
ValueError("Problem with line %s" % repr(line))
break
else:
line = handle.readline()
data += line
qual_len += len(line.strip())
if seq_len != qual_len:
raise ValueError("Problem with quality section")
return data
###############################################################################
_FormatToRandomAccess = {"ace" : SequentialSeqFileRandomAccess,
"embl" : EmblRandomAccess,
"fasta" : SequentialSeqFileRandomAccess,
"fastq" : FastqRandomAccess, #Class handles all three variants
"fastq-sanger" : FastqRandomAccess, #alias of the above
"fastq-solexa" : FastqRandomAccess,
"fastq-illumina" : FastqRandomAccess,
"genbank" : GenBankRandomAccess,
"gb" : GenBankRandomAccess, #alias of the above
"ig" : IntelliGeneticsRandomAccess,
"imgt" : EmblRandomAccess,
"phd" : SequentialSeqFileRandomAccess,
"pir" : SequentialSeqFileRandomAccess,
"sff" : SffRandomAccess,
"sff-trim" : SffTrimedRandomAccess,
"swiss" : SwissRandomAccess,
"tab" : TabRandomAccess,
"qual" : SequentialSeqFileRandomAccess,
"uniprot-xml" : UniprotRandomAccess,
}