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Parsing a sequence from a genbank file containing multiple sequences using Biopython SeqIO library

I have a genbank file containing a number or viral sequences. I am trying to parse through this file and print a single sequence by calling on its Locus name. The name of the sequence I am trying to access is "Abras_L_Seg_2". I am using the biopython function SeqIO. My code is as follows.

from Bio import SeqIO
record_dict = SeqIO.to_dict(SeqIO.parse("all.gb", "gb"))
print(record_dict['Abras_L_Seg_2'])

I am calling on this script via terminal and both my script and the genbank file are stored on the same level in the directory. This outputs this:

Traceback (most recent call last): File "practice_parsing.py", line 14, in <module> print(record_dict['Abras_L_Seg_2']) KeyError: 'Abras_L_Seg_2'

Any ideas?

rna-seq
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updated by Joe Joe • written by landonba • landonba

Please show us a minimal example of the genbank file.

I don't believe you can apply to_dict directly to a genbank file. The cookbook shows in section 5.4.1 that you instead need to do

records = SeqIO.to_dict(SeqIO.parse("/path/to/genbank.gb", "genbank")

You can then access the keys of the dictionary according to the id value. 

records['ID']

This is not the same as the LOCUS however, as it appears id comes from the VERSION field too (see section 4.2.3 of the cookbook).

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written by Joe Joe

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