Use ePost if you are familiar with Python. Have a look here for instructions.

EDIT: Here you have code that will do the job. In my computer it fetches 1k sequences every 20-30 seconds.

#!/usr/bin/env python
"""Fetch all entries for viridae from NCBI."""

import sys
from Bio      import Entrez
from datetime import datetime

Entrez.email = "your_email@gmail.com" 
query="viridae[Organism]"
db="nuccore"
retmax=10**9
retmode='fasta'
rettype='text'
batchSize=1000

#get list of entries for given query
sys.stderr.write( "Getting list of GIs for term=%s ...\n" % query )
handle = Entrez.esearch( db=db,term=query,retmax=retmax )
giList = Entrez.read(handle)['IdList']

#print info about number of proteins
sys.stderr.write( "Downloading %s entries from NCBI %s database in batches of %s entries...\n" % ( len(giList),db,batchSize ) )

#post NCBI query
search_handle     = Entrez.epost( db, id=",".join( giList ) )
search_results    = Entrez.read( search_handle )
webenv,query_key  = search_results["WebEnv"], search_results["QueryKey"] 

#fecth all results in batch of batchSize entries at once
for start in range( 0,len(giList),batchSize ):
  #print info
  tnow = datetime.now()
  sys.stderr.write( "\t%s\t%s / %s\n" % ( datetime.ctime(tnow),start,len(giList) ) )
  handle = Entrez.efetch( db=db,retmode=retmode,rettype=rettype,retstart=start,retmax=batchSize,webenv=webenv,query_key=query_key )
  sys.stdout.write( handle.read() )

You can do this fairly simply using ENA's advanced search facility as follows:

1. Go to the ENA homepage
2. Click on "Advanced search" to the right of the box labelled "text search" (should take you here)
3. Select the "Taxon" radio button. This will display a new section on the page, near the bottom, which allows you to narrow down your query. In your case, enter "viridae" next to "Taxon name = " and select the suggestion from the drop down. It should auto enter "tax_eq(10239)" in the query box at the top.
4. Click on "Search"
5. A results page will be displayed for each of the divisions of the nucleotide archive. I presume you want the original sequences, so click on the hyperlinked number in the column Taxon & decendants > Entries that corresponds with the row "Sequence (Release)" (currently, just over 1.5 million entries)
6. This will display a paginated list of all the ~1.5 million entries currently in ENA that are from that taxon (e.g. this page)
7. To download a fasta file of all the sequences, click on the "FASTA" link at the right hand side, top of the list, next to Download.

Hope this helps - I think it's preferential to do it this way, rather than scripting against a resource to get things one by one. I''m pretty sure it should be possible to do this at NCBI too but unfortunately, I don't use that resource. If you have any feedback about the usefulness/user-friendliness of this feature, please let the ENA team know

Thanks, Leszek. The example you point to includes a list of the GIs. I am not sure this would work with a list containing 1.3 million GIs

Hi everyone! I was trying to do something similar to Nick. I want to download GenBank results from 12S eukaryote. Since the normal website download does not work (I tried several times but I can get only 66% of the sequences) I wanted to try using the script Leszek posted. This is my code, slightly adjusted from Leszek:

enter code here#!/usr/bin/env python

import sys
from Bio      import Entrez
from datetime import datetime

faa_output = "12S_eukaryotesGB.txt" 
output_handle = open(faa_output, "w")
Entrez.email = "email@blabla.mail"
query='12S[All Fields] AND ("Eukaryota"[Organism] OR eukaryota[All Fields])' 
db="nucleotide"             
retmax=10**9
retmode='text'        
rettype='gb'        
batchSize=1000

#get list of entries for given query
sys.stderr.write( "Getting list of GIs for term=%s ...\n" % query )
handle = Entrez.esearch( db=db,term=query,retmax=retmax )      
giList = Entrez.read(handle)['IdList']

#print info about number of proteins
sys.stderr.write( "Downloading %s entries from NCBI %s database in batches of %s entries...\n" % ( len(giList),db,batchSize ) )     
#post NCBI query
search_handle     = Entrez.epost( db, id=",".join( giList ) )   
search_results    = Entrez.read( search_handle )
webenv,query_key  = search_results["WebEnv"], search_results["QueryKey"] 

#fecth all results in batch of batchSize entries at once
for start in range( 0,len(giList),batchSize ):      
  #print info
  tnow = datetime.now()
  sys.stderr.write( "\t%s\t%s / %s\n" % ( datetime.ctime(tnow),start,len(giList) ) )
  handle = Entrez.efetch( db=db,retmode=retmode,rettype=rettype,retstart=start,retmax=batchSize,webenv=webenv,query_key=query_key )
  #sys.stdout.write( handle.read() )        
  output_handle.write(handle.read())        
output_handle.close()       
print "Saved"

The script works great but after retrieving 4000/186000 results I get this error, which I do not understand:

Traceback (most recent call last): File "script_epost_fetch_sequences.py", line 41, in <module> output_handle.write(handle.read()) File "/usr/lib64/python2.7/socket.py", line 351, in read data = self._sock.recv(rbufsize)

File "/usr/lib64/python2.7/httplib.py", line 578, in read return self._read_chunked(amt)

File "/usr/lib64/python2.7/httplib.py", line 632, in _read_chunked raise IncompleteRead(''.join(value))

httplib.IncompleteRead: IncompleteRead(2450 bytes read)

Can anyone help me with this error?