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Problems with extracting genes from a genbank file using biopython

I am trying go extract the gene positions from a genbank file using Biopython. This is the function i wrote so far:

def get_CDS(file):
record = SeqIO.read(file, "genbank")
cds = []
for feature in record.features:
    if feature.type == 'CDS':
        print feature.location
        start_i = feature.location.start
        end_i = feature.location.end
        cds.append((start_i, end_i))
return cds

However I noticed sometimes, there are entries like: 

join{[4585844:4586295](-), [4584940:4585845](-)}

And then start and end positions will return: 4584940 and 4586295.

Does someone maybe know, how can I also get the positions of the genes accordingly, for the first part of the gene [4585844:4586295] and then [4584940:4585845]

gene genome biopython python
• 2,248 views • link
updated by Sej Modha Sej Modha • written by beginner_problem • beginner_problem

Could you please provide accession number of the genbank file you are trying to parse using this code?

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written by Sej Modha Sej Modha

For example, one of the pestis genomes causes this problem: NC_003143

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written by beginner_problem • beginner_problem

1 answer

Hi There,

I have used a sample genbank file here, the following should work for you too.

This produces following output.

['335:4642', '335:1838', '4586:5165', '5104:5396', '5376:7970', '5515:8199', '5607:5856', '5770:8341', '6918:7488', '8342:8963']
• 1 views • link
written by Sej Modha Sej Modha

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