Parse genbank file python

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Improve this answer. Gerrat Gerrat 27k 8 8 gold badges 68 68 silver badges 95 95 bronze badges. Need to revisit this: I tried my script on a different file: ncbi. Any ideas? Ryan Ryan 3, 1 1 gold badge 18 18 silver badges 31 31 bronze badges.

I had also previously had a line that would augment the count by 1 if a CDS feature was encountered. Depending on the type of GenBank file s you are interested in, they will either contain a single record, or multiple records. The following code uses Bio. In this case, there is actually only one record:. That example above uses a for loop and would cope with a GenBank file containing a multiple records.

The GenBank record's features property is a list of SeqFeature objects, each created from a feature in the original GenBank file. This is the twenty-seventh entry in the features list one based counting , and so its element 26 in the list zero based counting. How did I know this? Well, trial and error or by indexing the features. But anyway:. As you can see, this entry is for a CDS feature use.

To obtain the DNA sequence corresponding to complement CDS join Example of a single gene entry:. If two sequences contain overlapping fragment i. If there are two overlapping sequences. The interval from the beginning of one to the end of the other is capitalized. At4g F6N How it works. User Input.