Hello, biostars!
I have a list of GenBank specimen vouchers. Does anyone know some parser or script to get accession numbers and publications information about these sequences?
To make a table like:
Vouchers: VL03F635, WE02491
IDs: EF104615, AY557140, AY556740
References: Wiemers, 2003; Wiemers et al., 2010
It's not difficult to write a python script for that aim, but the problem is in GenBank records. Years and authors appear like different fields and i do not know how to process such a data.
1 answer
Hi Alice,
I was at a meeting last week where we decided to work on exactly this! If you wait a week or two we should have a tool to do this automatically in R.
Until then you should check out Biopython, and especially the genbank parser
from Bio import SeqIO
from Bio import Entrez
gb_ids = ["EF104615", "AY557140", "AY556740"]
query = Entrez.efetch(db="nucleotide", id=gb_ids, rettype="gb", retmode="text")
for rec in SeqIO.parse(query, "genbank"):
print(rec.id)
for paper in rec.annotations["references"]:
if paper.title != "Direct Submission":
print("{0} ({1})".format(paper.authors, paper.journal))
Check out the Bio.SeqFeature.Reference docs to see what is represented by these objects
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