[DAS] DAS client support for Python
Andrew Dalke
dalke@dalkescientific.com
Thu, 29 Aug 2002 01:23:33 -0600
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I've implemented a DAS client for Python. You can download
it at
http://www.biopython.org/~dalke/das.tar.gz
Here's some documentation for it.
- ungzip / untar it
- cd das
- start python
>>> import das
>>> server = das.Server("http://servlet.sanger.ac.uk:8080/das")
the 'server' object acts like a Python dictionary for the different
data sources available
>>> print len(server)
>>> print server.keys()
>>> dsn = server["mouse73"]
>>> sheet = dsn.stylesheet()
This is class is built given the DTD. Here's some examples of how
you can manipulate it.
Dump the whole data structure as XML
>>> print sheet
See what it contains
>>> sheet.get_children()
Work with subelements
>>> print len(sheet["STYLESHEET"])
>>> category = sheet["STYLESHEET"][0]
Get attributes of a node
>>> print category["TYPE"].id
>>> glyph = category["TYPE"]["GLYPH"]
Any subelement can also be dumped to XML
>>> print glyph
Get the text inside a node (.text() returns a list of unicode strings)
>>> print "".join(map(str, glyph[0]["COLOR"].text()))
Besides 'stylesheet' the following methods are also supported on a DSN
>>> [s for s in dir(dsn) if not s.startswith("_")]
['dna', 'dsn', 'entry_points', 'features', 'link', 'sequence', 'server', 'stylesheet', 'types']
(Actually, 'dsn' and 'server' are attributes.
>>> eps = dsn.entry_points()
>>> for segment in ep["ENTRY_POINTS"]:
... print segment.id, segment.size
...
X 147161770
19 61356199
18 91189200
17 94132929
16 99184200
15 104633288
14 116006794
13 117115093
12 114251360
11 122883361
10 131187037
9 125583845
8 129321983
7 135793178
6 150316567
5 151006098
4 151730910
3 160564582
2 180335396
1 196842934
>>> print dsn.dna( segments = [ ("X", 147161760, 147161770), ("1", 100, 20) ] )
Calling url 'http://servlet.sanger.ac.uk:8080/das/mouse73/dna' with query
'segment=X:147161760,147161770;segment=1:100,20'
<DASDNA>
<SEQUENCE start="147161760" version="7.3" stop="147161770" id="X">
<DNA length="11">
agagagagagt
</DNA>
</SEQUENCE>
<SEQUENCE start="100" version="7.3" stop="20" id="1">
<DNA length="81">
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnn
</DNA>
</SEQUENCE>
</DASDNA>
>>> print dsn.types( segments = [("6", None, None)] )
<DASTYPES>
<GFF href="http://servlet.sanger.ac.uk:8080/das/mouse73/types" version="1.0">
<SEGMENT start="1" version="7.3" stop="150316567" id="6">
<TYPE id="static_golden_path">
151
</TYPE>
<TYPE id="transcript">
23
</TYPE>
<TYPE id="translation">
23
</TYPE>
<TYPE id="exon">
304
</TYPE>
</SEGMENT>
</GFF>
</DASTYPES>
>>>
It also converts DAS errors into Python exceptions
>>> print dsn.sequence( [ ("X", 147161760, 147161770), ("1", 100, 20) ] )
Calling url 'http://servlet.sanger.ac.uk:8080/das/mouse73/sequence' with query
'segment=X:147161760,147161770;segment=1:100,20'
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "das.py", line 255, in sequence
return self._call("sequence", s, "dassequence")
File "das.py", line 243, in _call
return self.server._call(self.dsn + "/" + command, query, dtd_name)
File "das.py", line 180, in _call
raise DASError(status_code)
das.DASError: 400: Bad command (command not recognized)
>>>
Note that debugging is turned on in that it shows the URL called and
the query string, which gives you the chance to see what it's doing
and (if needed) reproduce a problem by hand.
Enjoy!
Andrew
dalke@dalkescientific.com
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--Multipart_Thu__29_Aug_2002_01:23:33_-0600_08442370--