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.
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__init__(self,
index_filename,
filenames,
format,
alphabet,
key_function,
max_open=10) |
source code
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keys(self)
Return a list of all the keys (SeqRecord identifiers). |
source code
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D[k] if k in D, else d
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get_raw(self,
key)
Similar to the get method, but returns the record as a raw string. |
source code
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Inherited from _IndexedSeqFileDict :
__setitem__ ,
__str__ ,
clear ,
copy ,
fromkeys ,
items ,
iteritems ,
iterkeys ,
itervalues ,
pop ,
popitem ,
update ,
values
Inherited from UserDict.DictMixin :
__cmp__ ,
has_key ,
setdefault
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