Access sequence element from fasta record using Biopython Entrez

Question 1

Here's what you need.

Instead of:

handle = Entrez.efetch(db='nuccore', id=key, rettype='fasta')

Try this:

handle = Entrez.efetch(db="nucleotide", id=key, retmode="xml") # retmode as 'xml' , db='nucleotide'
features = Entrez.read(handle)[0]
sequence = features['GBSeq_sequence'] # this is your sequence!

Which returns a character string that is your sequence:

'ggctcgcatctctccttcacgcgcccgccgccttacctgaggccgccatccacgccggttgagtcgcgttctgccgcctcccgcctgtggtgcctcctgaactacgtccgccgtctaggtaagtttagagctcaggtcgagaccgggcctttgtccggcgctcccttggagcctacctagactcagccggctctccacgctttgcctgaccctgcttgctcaactctacgtctttgtttcgttttctgttctgcgccgttacagatcgaaagttccacccctttccctttcattcacgactgactgccggcttggcccacggccaagtaccggcaactctgctggctcggagccagcgacagcccattctatagcactctccaggagagaaatttagtacacagttgggggctcgtccgggattcgagcgcccctttattccctaggcaatgggccaaatcttttcccgtagcgctagccctattccgcggccgccccgggggctggccgctcatcactggcttaacttcctccaggcggcatatcgcctagaacccggtccctccagttacgatttccaccagttaaaaaaatttcttaaaatagctttagaaacaccggtctggatctgccccattaactactccctcctagccagcctactcccaaaaggataccccggccgggtgaatgaaattttacacatactcatccaaacccaagcccagatcccgtcccgccccgcgccgccgccgccgtcatcctccacccacgaccccccggattctgacccacaaatcccccctccctatgttgagcctacagccccccaagtccttccagtcatgcacccacatggtgcccctcccaaccaccgcccatggcaaatgaaagacctacaggccattaagcaagaagtctcccaagcggcccctggaagcccccagtttatgcagaccatccggcttgcggtgcagcagtttgaccccactgccaaagacctccaagacctcctgcagtacctttgctcctccctcgtggcttccctccatcaccagcagctagatagccttatatcagaggccgaaactcgaggtattacaggttataaccccttagccggtcccctccgtgtccaagccaacaatccacaacaacaaggattaaggcgagaataccagcaactctggctcgccgccttcgccgccctgccagggagtgccaaagacccttcctgggcctctatcctccaaggcctggaggagccttaccacgccttcgtagaacgcctcaacatagctcttgacaatgggctgccagaaggcacgcccaaagaccccattttacgttccttagcctactctaatgcaaacaaagaatgccaaaaattactacaggcccgagggcacactaatagccctctaggagatatgttgcgggcttgtcaggcctggacccccaaagacaaaaccaaagtgttagttgtccagcctaaaaaaccccccccaaatcagccgtgcttccggtgcgggaaagcaggccactggagtcgggactgcactcagcctcgtcctccccctgggccatgccccctatgtcaagatccaactcactggaagcgagactgcccccgcctaaagcccactatcccagaaccagagccagaggaggatgccctcctattagatctccccgccgacatcccacacccaaaaaactccatagggggggaggtttaacctccccccccacattacagcaagtccttcctaaccaagacccaacatctattctgccagttataccgttagatcccgcccgtcggcccgtaattaaagcccagattgacacccagaccagccacccaaagactatcgaagctctactagatacaggagcagacatgacagtccttccgatagccttgttctcaagtaatactcccctcaaaaacacatccgtgttaggggcagggggccaaacccaagatcactttaagctcacctcccttcctgtgctaatacgcctccctttccggacgacgcctattgttttaacatcttgcctagttgataccaaaaacaactgggccatcataggtcgtgatgccttacaacaatgccaaggcgtcctgtacctccctgaggcaaaaaggccgcctgtaatcttgccaatacaggcgccagctgtccttgggctagaacacctcccaaggccccccgaaatcagccagttccctttaaaccagaacgcctccaggccttgcaacacttggtccggaaggccctggaggcaggccatatcgaaccctacaccgggccaggaaataacccagtattcccagttaaaaaagccaatggaacctggcgattcatccacgacctgcgggccactaactctctaaccatagatctctcatcatcttcccccgggccccctgacttgtccagcctgccaactacactagcccacttacaaactatagaccttaaagacgcctttttccaaatccccctacctaaacagttccagccctactttgctttcactgtcccacagcagtgtaactacggccccggcactagatacgcctggagagtactaccccaagggtttaaaaatagtcccaccctgttcgaaatgcagctggcccatatcctgcagcccattcggcaagccttcccccaatgcactattcttcagtacatggatgacattctcctggcaagcccctcccatgcggacctgcaactactctcagaggccacaatggcttccctaatctcccatgggttgcctgtgtccgaaaacaaaacccagcaaacccctggaacaattaagttcctagggcaaataatttcacctaatcacctcacttatgatgcagtccccaaggtacctatacggtcccgctgggcgctacctgaacttcaagccctacttggcgagattcagtgggtctccaaaggaactcctaccttacgccagccccttcacagtctctactgtgccttacaaaggcatactgatccccgagaccaaatatatttaaatccttctcaagttcaatcattagtgcagctgcggcaggccctgtcacagaactgccgcagtagactagtccaaaccctgcccctcctaggggctattatgctgaccctcactggcaccaccactgtggtgttccagtccaagcagcagtggccacttgtctggctacatgcccccctaccccacactagccagtgcccctgggggcagctacttgcctcagctgtgttattactcgacaaatacaccttgcaatcctatggactactctgccaaaccatacatcataacatctccacccaaaccttcaaccaattcattcaaacatctgaccaccccagtgttcctatcttactccaccacagtcaccgattcaaaaatttaggtgcccagactggagaactttggaacacttttcttaaaacaactgccccattggctcctgtgaaagcccttatgccagtgtttactctttcccctgtgatcataaacaccgccccttgcctgttttcagacggatccacctcccaggcagcctatattctctgggacaagcatatattgtcacaaagatcattcccccttccgccaccgcacaagtcggcccaacgggccgaacttctcggacttttgcatggcctctccagcgcccgttcgtggcgctgtctcaacatatttctagactccaagtatctttatcattaccttcggacccttgccctaggcaccttccaaggcaggtcctctcaggccccctttcaggccctcctgccccgcttactatcgcgtaaggtcgtctatttgcaccacgttcgcagccataccaatctacctgatcccatctccaggctcaacgctctcacagatgccctactaatcacccctgtcctgcagctctctcctgcagacctacacagtttcacccattgcggacagacggccctcacactgcaaggggcaaccacaactgaggcctccaatatcctgcgctcttgccacgcctgccgcaaaaataacccacaacatcagatgcctcaaggacacatccgccgtggcctactccctaaccacatctggcaaggcgacattacccatttcaaatataaaaatacactgtatcgccttcatgtatgggtagacaccttttcaggagccatctcagctacccaaaagagaaaagaaacaagctcagaagctatttcctctttgctccaggccattgcctatctaggcaagcctagctacataaacacagacaatggccctgcctatatttcccaagacttcctcaatatgtgtacctcccttgctattcgccatactacccatgtcccctacaatccaaccagctccggacttgtagaacgctctaatggcattcttaaaaccctattatataagtactttactgacaaacccgacctacctatggataatgctctatccatagccctatggacaatcaaccacctaaatgtattaaccaactgccacaaaacccgatggcagcttcaccactccccccgactccagccgatcccagagacacattccctcagcaataaacaaacccattggtattatttcaagcttcctggtcttaatagccgccagtggaaaggaccacaggaggctcttcaagaagctgccggcgctgctctcatcccggtaagcgctagttctgcccagtggatcccgtggaggctcctcaagcgagctgcatgcccaagacccgtcggaggccccgccgatcccaaagaaaaagaccaccaacaccatgggtaagtttctcgccactttgattttattcttccagttctgccccctcatcctcggtgattacagccccagctgctgtactctcacagttggagtctcctcataccactctaaaccctgcaatcctgcccagccagtttgttcatggaccctcgacctgctggccctttcagcagatcaggccctacagccaccctgccctaatctagtaagttactccagctaccatgccacctattccctatatctattccctcattggatcaaaaagccaaaccgaaatggcggaggctattattcagcctcttattcagacccttgttccttaaaatgcccatacctagggtgccaatcatggacctgcccctatacaggagccgtctccagcccctactggaaatttcagcaagatgtcaattttactcaagaagtttcacacctcaatattaatctccatttttcaaaatgcggtttttccttctcccttctagtcgacgctccaggatatgaccccatctggttccttaataccgaacccagccaactgcctcccaccgcccctcctctactctcccactctaacctagaccatatcctcgagccctctataccatggaaatcaaaactcctgactcttgtccagttaaccctacaaagcactaattatacttgcattgtctgtatcgatcgtgccagcctatccacttggcacgtcctatactctcccaacgtctctgttccatccccttcttctacccccctcctttacccatcgttagcgcttccagccccccacctgacgttaccatttaactggacccactgctttgacccccagattcaagctatagtctcctccccctgtcataactccctcatcctgccccccttttccttgtcacctgttcccacgctaggatcccgctcccgccgagcagtaccggtggcggtctggcttgtctccgccctggccatgggagccggagtggctggcaggattaccggctccatgtccctcgcctcaggaaagagcctcctacatgaggtggacaaagatatttcccaattaactcaagcaatagtcaaaaaccacaaaaatctgctcaaaattgcacagtatgctgcccagaacagacgaggccttgatctcctgttctgggagcaaggaggattatgcaaagcattacaagaacagtgctgttttctaaatattactaattcccatgtctcaatactacaagagagacccccccttgaaaatcgagtcctgactggctggggccttaactgggaccttggcctctcacagtgggctcgagaagccttacaaactggaatcacccttgtcgcgctactccttcttgttatccttgcaggaccatgcatcctccgtcagctacgacacctcccctcgcgcgtcagatacccccattactctcttataaaccctgagtcatccctgtaaaccaagcacacaattattgcaaccacatcgcctccagcctcccctgccaataattaacctctcccatcaaatcctccttctcctgcagcaacctcctccgttcagcctccaaggactccacctcgccttccaactgtctagtatagccatcaacccccaactcctgcattttttctttcctagcactatgctgtttcgccttctcagccccttgtctccacttgcgctcacggcgctcctgctcttcctgctttctccgggcgaagtcagcggccttctcctccgcccgcttcctgcgccgtgccttctcctcttccttccttttcaaatactcagcaatctgcttttcctcctctttctcccgctctttttttcgcttcctcttctcctcagcccgtcgctgccgatcacgatgcgtttccccgcgaggtggcgctttcccccctggagggccccgtcgcagccggccgcggctttcctcttctagagatagcaaaccgtcaagcacagtttcctcctcctccttgtcctttaactcttcctccaaggataatagcccgtccaccaattcctccaccagcaggtcctccgggcatggaacaggcaaacatcgaaacagccctacggatacaaagttaaccatgcttattatcagcccacttcccagggtttggacagagtcttcttttcggatacccagtctacgtgtttggagactgtgtacaaggcgactggtgccccatctctgggggactatgttcggcccgcctacatcgtcacgccctactggccacctgtccagagcatcagatcacctgggaccccatcgatggacgcgttatcggctcagctctacagttccttatccctcgactcccctccttccccacccagagaacctctaagacccttaaggtccttaccccgccaatcactcatacaacccccaacattccaccctccttcctccaggccatgcgcaaatactcccccttccgaaatggatacatggaacccacccttgggcagcacctcccaaccctgtcttttccagaccccggactccggccccaaaacctgtacaccctctggggaggctccgttgtctgcatgtacctctaccagctttccccccccatcacctggcccctcctgccccatgtgattttttgccaccccggccagctcggggccttcctcaccaatgttccctacaaacgaatagaaaaactcctctataaaatttcccttaccacaggggccctaataattctacccgaggactgtttgcccaccacccttttccagcctgctagggcacccgtcacgctgacagcctggcaaaacggcctccttccgttccactcaaccctcaccactccaggccttatttggacatttaccgatggcacgcctatgatttccgggccctgccctaaagatggccagccatctttagtactacagtcctcctcctttatatttcacaaatttcaaaccaaggcctaccacccctcatttctactctcacacggcctcatacagtactcttcctttcataatttgcatctcctatttgaagaatacaccaacatccccatttctctactttttaacgaaaaagaggcagatgacaatgaccatgagccccaaatatcccccgggggcttagagcctctcagtgaaaaacatttccgtgaaacagaagtctgagaaggtcagggcccagaataaggctctgacgtctccccccggaggacagctcagcaccagctcaggctaggccctgacgtgtccccctaaagacaaatcataagctcagacctccgggaagccaccgggaaccacccatttcctccccatgtttgtcaagccgtcctcaggcgttgacgacaacccctcacctcaaaaaacttttcatggcacgcatacggctcaataaaataacaggagtctataaaagcgtggggacagttcaggagggggctcgcatctctccttcacgcgcccgccgccttacctgaggccgccatccacgccggttgagtcgcgttctgccgcctcccgcctgtggtgcctcctgaactacgtccgccgtctaggtaagtttagagctcaggtcgagaccgggcctttgtccggcgctcccttggagcctacctagactcagccggctctccacgctttgcctgaccctgcttgctcaactcta'

Question 2

I'm fairly certain that when you use biopython to parse the fasta file, it organizes the information into a dictionary of dictionaries. You can check how everything is organized yourself by printing

print dir(seq_record)

I know that when parsing a genbank file, each seq_record has a dictionary called features, so for a FASTA file, assuming it is organized the same way you can access just the sequence by the following

for record in SeqIO.parse(handle, "fasta"):
    for f in record.features:
        print "sequence"
        print dir(f) # Print the attributes of f to make sure that "sequence" used in the above line is in fact a key in the dictionary, if not pick the correct key to use above