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Base code for representing a database source of sequences.
This module contains code which can be used to describe a specialized
location where sequence information is available from. The code here
covers the basic cases (ie. a CGI script to retrieve information from)
as classes (CGI, in our example) which need to be supplied the database
specific information. So, if you want to programmatically describe
a database, this is the place to start looking for useful classes.
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Imported modules
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from Bio import StdHandler, SeqRecord
from Bio.ReseekFile import ReseekFile
from Bio.Tools.MultiProc.copen import copen_fn
from Bio.WWW import RequestLimiter
from Martel import Parser
import StringIO
import operator
import time
import urllib
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Functions
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_my_urlencode
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_my_urlencode
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_my_urlencode ( params )
urllib only handles key=value pairs. However, some CGI
scripts also contain parameters that are passed without the
key= part. Thus, search through the params for empty
strings (or None), and handle these myself.
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Classes
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| BioCorba |
Represent a BioCorba BioSequenceCollection for SeqRecord objects.
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| BioSQL |
Represent a BioSQL-style database to retrieve SeqRecord objects.
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| CGI |
cgi
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| IndexedFile |
Return SeqRecord objects from an indexed file.
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| Source |
Base class for representing a database source.
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