[BioPython] script to extract records from nucleotide database
Christof Winter
winter at biotec.tu-dresden.de
Tue Nov 13 20:25:45 UTC 2007
Matthew Abravanel wrote:
> Hi Christof,
>
> I tried out the code you sent me just to see if it would work but I get an
> attribute error or something? Here is the error I get:
>
>
> Traceback (most recent call last):
> File "./run", line 3, in ?
> from Bio import GenBank
> File "/usr/pkg/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line
> 47, in ?
> File "/usr/pkg/lib/python2.4/site-packages/Bio/GenBank/Scanner.py", line
> 20, in ?
> from Bio.SeqRecord import SeqRecord
> File "/usr/pkg/lib/python2.4/site-packages/Bio/SeqRecord.py", line 11, in
> ?
> File "/usr/pkg/lib/python2.4/site-packages/Bio/FormatIO.py", line 55, in
> __init__
> AttributeError: 'module' object has no attribute 'formats'
Hi Matthew,
your import of the GenBank module fails. Most likely your BioPython installation
is broken. Could you try to re-install it?
On a Python (2.4) shell, this should work:
Python 2.4.4 (#2, Apr 5 2007, 20:11:18)
[GCC 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> import Bio.GenBank
>>>
HTH,
Christof
>
>
> Here is the code I have used:
>
>
>
> #!/usr/pkg/bin/python2.4
>
> from Bio import GenBank
>
>
> featureParser = GenBank.FeatureParser()
> ncbiDict = GenBank.NCBIDictionary("nucleotide",
> "genbank",parser=featureParser)
>
> accessionNumbers=["BC063166", "NM_028459"]
>
>
> for accessionNo in accessionNumbers:
> giList = GenBank.search_for(accessionNo)
> for gi in giList:
> record = ncbiDict[gi]
> for feature in record.features:
> if feature.type =="CDS":
> codingStart = feature.location._start.position
> codingEnd = feature.location._end.position
> completeSequence = record.seq.tostring()
> fiveUTRSequence = completeSequence[:codingStart]
> codingSequence = completeSequence[codingStart:codingEnd]
> threeUTRSequence = completeSequence[codingEnd:]
> if feature.type=="gene":
> geneName=feature.qualifiers['gene'][0]
>
> print "Found",gi,geneName,len(completeSequence)
>
>
> I do not know if it is a difference in python2.4 version or not? Any help
> would be appreciate, thanks.
>
> Matthew
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