[BioPython] script to extract records from nucleotide database

[Matthew Abravanel]

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'


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