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import os
import Bio
import compression
def _int_str(i):
s = str(i)
if s[-1:] == "l":
return s[:-1]
return s
class WriteDB:
# Must define 'self.filename_map' mapping from filename -> fileid
# Must define 'self.fileid_info' mapping from fileid -> (filename,size)
def add_filename(self, filename, size, fileid_info):
fileid = self.filename_map.get(filename, None)
if fileid is not None:
return fileid
s = str(len(self.filename_map))
self.filename_map[filename] = s # map from filename -> id
assert s not in fileid_info.keys(), "Duplicate entry! %s" % (s,)
self.fileid_info[s] = (filename, size)
return s
def load(self, filename, builder, fileid_info, record_tag = "record"):
formatname = self.formatname
size = os.path.getsize(filename)
filetag = self.add_filename(filename, size, fileid_info)
source = compression.open_file(filename, "rb")
if formatname == "unknown":
formatname = "sequence"
format = Bio.formats.normalize(formatname).identifyFile(source)
if format is None:
raise TypeError("Cannot identify file as a %s format" %
(self.formatname,))
if self.formatname == "unknown":
expected_names = ["fasta", "embl", "swissprot", "genbank"]
for node in format._parents:
if node.name in expected_names:
self.formatname = node.name
break
else:
self.formatname = format.name
iterator = format.make_iterator(
record_tag,
select_names = tuple(builder.uses_tags()) + (record_tag,),
debug_level = 0)
for record in iterator.iterate(source, cont_handler = builder):
self.add_record(filetag,
iterator.start_position,
iterator.end_position - iterator.start_position,
record.document)
class DictLookup:
def __getitem__(self, key):
raise NotImplementedError("Must be implemented in subclass")
def keys(self):
raise NotImplementedError("Must be implemented in subclass")
def values(self):
return [self[key] for key in self.keys()]
def items(self):
return [(key, self[key]) for key in self.keys()]
def get(self, key, default = None):
try:
return self[key]
except KeyError:
return default
class OpenDB(DictLookup):
def __init__(self, dbname, index_type):
self.dbname = dbname
config = read_config(os.path.join(dbname, "config.dat"))
if config["index"] != index_type:
raise TypeError("FlatDB does not support %r index" %
(config["index"],))
self.primary_namespace = config["primary_namespace"]
self.secondary_namespaces = config["secondary_namespaces"]
self.formatname = config["format"]
filename_map = {}
fileid_info = {}
for k, v in config.items():
if not k.startswith("fileid_"):
continue
fileid = k[7:]
filename, size = v
fileid_info[fileid] = v
filename_map[filename] = fileid
if os.path.getsize(filename) != size:
raise TypeError(
"File %s has changed size from %d to %d bytes!" %
(size, os.path.getsize(filename)))
self.filename_map = filename_map
self.fileid_info = fileid_info
def lookup(self, *args, **kwargs):
if args:
if kwargs:
raise TypeError("Cannot specify both args and kwargs")
if len(args) != 1:
raise TypeError("Only one identifier handled")
namespace, name = self.primary_namespace, args[0]
else:
if len(kwargs) != 1:
raise TypeError("lookup takes a single key")
namespace, name = kwargs.items()[0]
return self[namespace][name]
def __getitem__(self, namespace):
"""return the database table lookup for the given namespace"""
raise NotImplementedError("must be implemented in the derived class")
def keys(self):
return [self.primary_namespace] + self.secondary_namespaces
# Write the configuration
def write_config(config_filename,
index_type,
primary_namespace,
secondary_namespaces,
fileid_info,
formatname):
configfile = open(config_filename, "wb")
# Write the header
configfile.write("index\t" + index_type + "\n")
# Write the namespace information
configfile.write("primary_namespace\t%s\n" % primary_namespace)
keys = secondary_namespaces[:]
keys.sort()
configfile.write("secondary_namespaces\t")
configfile.write("\t".join(keys) + "\n")
# Format name
configfile.write("format\t" + formatname + "\n")
# Write the fileid table
items = fileid_info.items()
items.sort()
for fileid, (filename, size) in items:
configfile.write("fileid_%s\t%s\t%s\n" % \
(fileid, filename, _int_str(size)))
configfile.close()
def read_config(config_filename):
d = {}
for line in open(config_filename, "rb").read().split("\n"):
words = line.rstrip().split("\t")
assert not d.has_key(words[0]), \
"Duplicate key %r in config file: old = %r, new = %r" % \
(words[0], d[words[0]], line)
if words[0] in ("index", "primary_namespace", "format"):
if len(words) != 2:
raise AssertionError(
"%s should only have one value, not %r" % \
(words[0], words[1:]))
d[words[0]] = words[1]
elif words[0].startswith("fileid_"):
if len(words) != 3:
raise AssertionError(
"%s should only have two values, not %r" % \
(words[0], words[1:]))
d[words[0]] = (words[1], long(words[2]))
elif words[0] in ("secondary_namespaces",):
# This can have 0 or more values
d[words[0]] = words[1:]
else:
# Unknown word, save as-is
d[words[0]] = words[1:]
return d
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