[BioPython] Problem using GenBank.Dictionary
Michael Sorich
mike_sorich@hotmail.com
Thu, 16 May 2002 14:11:14 +0930
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Hi
=20
I am having some trouble making a GenBank database (using an index file
and GenBank.Dictionary). I can use an GenBank.Iterator to parse through
genbank records in a file, however, if I make a GenBank database of the
file and then request a particular record, I get a parsing error
=93ParserPositionException: error parsing at or beyond character 0=94. =
The
dictionary seems to be created properly (ie it has keys corresponding to
all the records in the file) and the error only occurs when I call for a
particular record.
=20
I have included an example below, parsing a file containing only 1
genbank record into a FeatureRecord using a GenBank.Iterator (which
works) and then a GenBank.Dictionary (which does not work). I would
appreciate it if someone could let me know where I have gone wrong.=20
=20
--Script
from Bio import GenBank
=20
gb_file =3D "C:\\Documents and Settings\\MikeUser\\Desktop\\Z71185.gb"
=20
#first parse using GenBank.Iterator
gb_handle =3D open(gb_file, 'r')
parser =3D GenBank.FeatureParser()
gb_iterator =3D GenBank.Iterator(gb_handle, parser)
cur_record =3D gb_iterator.next()
if cur_record:
print dir(cur_record)
print "Accession No is", cur_record.id
=20
#now parse with GenBank.Dictionary
indexFile =3D 'Z71185.idx'
GenBank.index_file(gb_file, indexFile)
gbDict =3D GenBank.Dictionary(indexFile, GenBank.FeatureParser())
print "keys in dictionary =3D",gbDict.keys()
cur_record =3D gbDict['Z71185']
if cur_record:
print dir(cur_record)
print "Accession No is", cur_record.id
=20
--Output
['annotations', 'description', 'features', 'id', 'name', 'seq']
Accession No is Z71185.1
keys in dictionary =3D ['Z71185']
Traceback (most recent call last):
File "C:\PROGRA~1\Python21\Pythonwin\pywin\framework\scriptutils.py",
line 396, in ImportFile
reload(sys.modules[modName])
File "C:\Documents and Settings\MikeUser\My
Documents\Python\scripts\testGenbank.py", line 19, in ?
=20
File "c:\progra~1\python21\Bio\GenBank\__init__.py", line 114, in
__getitem__
return self._parser.parse(File.StringHandle(data))
File "c:\progra~1\python21\Bio\GenBank\__init__.py", line 268, in
parse
self._scanner.feed(handle, self._consumer)
File "c:\progra~1\python21\Bio\GenBank\__init__.py", line 1250, in
feed
self._parser.parseFile(handle)
File "c:\progra~1\python21\Martel\Parser.py", line 230, in parseFile
self.parseString(fileobj.read())
File "c:\progra~1\python21\Martel\Parser.py", line 258, in parseString
self._err_handler.fatalError(result)
File "c:\progra~1\python21\lib\xml\sax\handler.py", line 38, in
fatalError
raise exception
ParserPositionException: error parsing at or beyond character 0
=20
=20
Thanks
=20
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: michael.sorich@postgrads.unisa.edu.au
mike_sorich@hotmail.com
=20
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<body lang=3DEN-AU link=3Dblue vlink=3Dpurple =
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<div class=3DSection1>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Hi<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I am having some trouble making a <span =
class=3DSpellE>GenBank</span>
database (using an index file and <span =
class=3DSpellE>GenBank.Dictionary</span>).
I can use an <span class=3DSpellE>GenBank.Iterator</span> to parse =
through <span
class=3DSpellE>genbank</span> records in a file, however, if I make a =
<span
class=3DSpellE>GenBank</span> database of the file and then request a =
particular
record, I get a parsing error =93<span =
class=3DSpellE>ParserPositionException</span>:
error parsing at or beyond character 0=94. The dictionary seems to be
created properly (<span class=3DSpellE>ie</span> it has keys =
corresponding to all
the records in the file) and the error only occurs when I call for a =
particular
record.<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I have included an example below, parsing a file =
containing
only 1 <span class=3DSpellE>genbank</span> record into a <span =
class=3DSpellE>FeatureRecord</span>
using a <span class=3DSpellE>GenBank.Iterator</span> (which works) and =
then a <span
class=3DSpellE>GenBank.Dictionary</span> (which does not work). I would
appreciate it if someone could let me know where I have gone wrong. =
<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>--Script<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>from</span></font></span><fo=
nt
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> Bio import <span
class=3DSpellE>GenBank</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>gb_file</span></font></span>=
<font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D
"C:\\Documents and =
Settings\\MikeUser\\Desktop\\Z71185.gb"<o:p></o:p></span></font></p>=
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>#first parse using <span =
class=3DSpellE>GenBank.Iterator</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>gb_handle</span></font></spa=
n><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D <span
class=3DGramE>open(</span><span class=3DSpellE>gb_file</span>, =
'r')<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>parser</span></font></span><=
font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D <span
class=3DSpellE>GenBank.FeatureParser</span>()<o:p></o:p></span></font></p=
>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>gb_iterator</span></font></s=
pan><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D <span
class=3DSpellE><span class=3DGramE>GenBank.Iterator</span></span><span =
class=3DGramE>(</span><span
class=3DSpellE>gb_handle</span>, parser)<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>cur_record</span></font></sp=
an><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D <span
class=3DSpellE>gb_<span class=3DGramE>iterator.next</span></span><span =
class=3DGramE>()</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>if</span></font></span><font=
size=3D2
face=3DArial><span style=3D'font-size:10.0pt;font-family:Arial'> <span
class=3DSpellE>cur_record</span>:<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DGramE>print</span> dir(<span =
class=3DSpellE>cur_record</span>)<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DGramE>print</span> "Accession No is", <span =
class=3DSpellE>cur_record.id</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>#now <span class=3DGramE>parse</span> with <span =
class=3DSpellE>GenBank.Dictionary</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><span class=3DGramE><font =
size=3D2
face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>indexFile</span></font></spa=
n></span><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D
'Z71185.idx'<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>GenBank.index_<span =
class=3DGramE>file</span></span></font></span><span
class=3DGramE><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:
Arial'>(</span></font></span><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>gb_file</span></font></span>=
<font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>, <span
class=3DSpellE>indexFile</span>)<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><span class=3DGramE><font =
size=3D2
face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>gbDict</span></font></span><=
/span><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D <span
class=3DSpellE>GenBank.Dictionary</span>(<span =
class=3DSpellE>indexFile</span>, <span
class=3DSpellE>GenBank.FeatureParser</span>())<o:p></o:p></span></font></=
p>
<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>print</span></font></span><f=
ont
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> "keys
in dictionary =3D",<span =
class=3DSpellE>gbDict.keys</span>()<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>cur_record</span></font></sp=
an><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> =3D <span
class=3DSpellE><span class=3DGramE>gbDict</span></span><span =
class=3DGramE>[</span>'Z71185']<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>if</span></font></span><font=
size=3D2
face=3DArial><span style=3D'font-size:10.0pt;font-family:Arial'> <span
class=3DSpellE>cur_record</span>:<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DGramE>print</span> dir(<span =
class=3DSpellE>cur_record</span>)<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DGramE>print</span> "Accession No is", <span =
class=3DSpellE>cur_record.id</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>--Output<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>['annotations', 'description', 'features', 'id', =
'name', '<span
class=3DSpellE>seq</span>']<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Accession No is Z71185.1<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DGramE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>keys</span></font></span><fo=
nt
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> in
dictionary =3D ['Z71185']<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>Traceback</span></font></spa=
n><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'> (most
recent call last):<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"C:\PROGRA~1\Python21\Pythonwin\pywin\framework\scriptutils.py"=
, line
396, in <span =
class=3DSpellE>ImportFile</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DGramE>reload(</span><span =
class=3DSpellE>sys.modules</span>[<span
class=3DSpellE>modName</span>])<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"C:\Documents and Settings\<span class=3DSpellE>MikeUser</span>\My
Documents\Python\scripts\<span =
class=3DSpellE>testGenbank.py</span>", line
19, <span class=3DGramE>in ?</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"c:\progra~1\python21\Bio\GenBank\__init__.py", line 114, in =
__<span
class=3DSpellE>getitem</span>__<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DGramE>return</span> <span =
class=3DSpellE>self._parser.parse</span>(<span
class=3DSpellE>File.StringHandle</span>(data))<o:p></o:p></span></font></=
p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"c:\progra~1\python21\Bio\GenBank\__init__.py", line 268, in =
parse<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DSpellE>self._<span class=3DGramE>scanner.feed</span></span><span
class=3DGramE>(</span>handle, <span =
class=3DSpellE>self._consumer</span>)<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"c:\progra~1\python21\Bio\GenBank\__init__.py", line 1250, in =
feed<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DSpellE>self._<span =
class=3DGramE>parser.parseFile</span></span><span
class=3DGramE>(</span>handle)<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"c:\progra~1\python21\Martel\Parser.py", line 230, in <span
class=3DSpellE>parseFile</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DSpellE><span class=3DGramE>self.parseString</span></span><span =
class=3DGramE>(</span><span
class=3DSpellE>fileobj.read</span>())<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"c:\progra~1\python21\Martel\Parser.py", line 258, in <span
class=3DSpellE>parseString</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DSpellE>self._err_<span =
class=3DGramE>handler.fatalError</span></span><span
class=3DGramE>(</span>result)<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> </span>File
"c:\progra~1\python21\lib\xml\sax\handler.py", line 38, in =
<span
class=3DSpellE>fatalError</span><o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><span style=3D'mso-spacerun:yes'> =
</span><span
class=3DGramE>raise</span> exception<o:p></o:p></span></font></p>
<p class=3DMsoNormal><span class=3DSpellE><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>ParserPositionException</spa=
n></font></span><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>: error
parsing at or beyond character 0<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Thanks<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Michael =
Sorich<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>PhD =
Student<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>School of Pharmaceutical, Molecular =
and
Biomedical Sciences<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>University of South =
Australia<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Email:
michael.sorich@postgrads.unisa.edu.au<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style=3D'mso-spacerun:yes'> &nbs=
p;
</span>mike_sorich@hotmail.com<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p> </o:p></span></font></p>
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