Hi All,

I have a list of bioproject IDs and would like to get corresponding sequences from them. So, I am following a list of steps as below:

1. Using the bioproject ID, I am getting GI ID using elink:

handle = Entrez.elink(dbfrom="bioproject", db="nuccore",id=bioprojecID, linkname="bioproject_nuccore_wgsmaster")
record = Entrez.read(handle)
GI_ID = record[0]["LinkSetDb"]["Link"]["Id"]

2. Then I am trying to get sequence from GI_ID (using efetch and seqIO modules in biopython):

handle = Entrez.efetch(db="nucleotide", id=GI_ID, rettype="gb", retmode="text")
record = SeqIO.read(handle, "genbank")

But this gives unknown sequence when trying to print record.

Can anyone advise if this is the right way to do it or is there a better way to obtain related sequences from bioproject IDs?

Thanks in advance!

I can help with SeqIO part. Assuming that your "handle" is a genbank file.

from Bio import SeqIO

for record in SeqIO.parse(open(handle), 'genbank'):
    print record.id, record.seq

For more options do this:

print dir(record)
break

This will return a list of methods you can call on record object - that way you can get different information about your file (handle)