In [1]:

    

from Bio import Entrez, Seq, SeqIO
from Bio.Alphabet import IUPAC


    

In [2]:

    

Entrez.email = "put@your_email.here" 
hdl = Entrez.efetch(db='nucleotide', id=['NM_002299'], rettype='fasta')  # Lactase gene
#for l in hdl:
#    print l
seq = SeqIO.read(hdl, 'fasta')


    

In [3]:

    

w_seq = seq[11:5795]
w_seq


    

    
Out[3]:





SeqRecord(seq=Seq('ATGGAGCTGTCTTGGCATGTAGTCTTTATTGCCCTGCTAAGTTTTTCATGCTGG...TGA', SingleLetterAlphabet()), id='gi|32481205|ref|NM_002299.2|', name='gi|32481205|ref|NM_002299.2|', description='gi|32481205|ref|NM_002299.2| Homo sapiens lactase (LCT), mRNA', dbxrefs=[])

In [4]:

    

w_hdl = open('example.fasta', 'w')
SeqIO.write([w_seq], w_hdl, 'fasta')
w_hdl.close()


    

In [5]:

    

recs = SeqIO.parse('example.fasta', 'fasta')
for rec in recs:
    print(type(rec))
    seq = rec.seq
    print(rec.description)
    print(seq[:10])
    print(seq.alphabet)


    

    




<class 'Bio.SeqRecord.SeqRecord'>
gi|32481205|ref|NM_002299.2| Homo sapiens lactase (LCT), mRNA
ATGGAGCTGT
SingleLetterAlphabet()

In [6]:

    

seq = Seq.Seq(str(seq), IUPAC.unambiguous_dna)
seq


    

    
Out[6]:





Seq('ATGGAGCTGTCTTGGCATGTAGTCTTTATTGCCCTGCTAAGTTTTTCATGCTGG...TGA', IUPACUnambiguousDNA())

In [7]:

    

print((seq[:12], seq[-12:]))
rna = seq.transcribe()
rna


    

    




(Seq('ATGGAGCTGTCT', IUPACUnambiguousDNA()), Seq('TCTTCATTCTGA', IUPACUnambiguousDNA()))






    
Out[7]:





Seq('AUGGAGCUGUCUUGGCAUGUAGUCUUUAUUGCCCUGCUAAGUUUUUCAUGCUGG...UGA', IUPACUnambiguousRNA())

In [8]:

    

prot = seq.translate()
prot


    

    
Out[8]:





Seq('MELSWHVVFIALLSFSCWGSDWESDRNFISTAGPLTNDLLHNLSGLLGDQSSNF...SF*', HasStopCodon(IUPACProtein(), '*'))

In [8]: