Problem solved with BioPython! Thanks for the help.

Edit, here's my code:

# command line usage: python entrez.py database searchterm output.fasta

from Bio import Entrez, SeqIO
import sys
import os

dataBase = sys.argv[1]
searchTerm = sys.argv[2]
outFile = sys.argv[3]

Entrez.email = "your.email@goes.here"
handle = Entrez.esearch(db = dataBase, retmax = 100000, term = searchTerm)
record = Entrez.read(handle)
handle.close()
with open(outFile, 'w') as w:
    for id in record["IdList"]:
        fetch_handle = Entrez.efetch(db = dataBase, id = id, rettype = "fasta", retmode="text")
        fetch_record = SeqIO.read(fetch_handle, "fasta")
        fetch_handle.close()
        SeqIO.write(fetch_record, "current_seq.fasta", "fasta")
        for line in open('current_seq.fasta'):
            w.write(line)
os.remove("current_seq.fasta")