I have a list of refseq IDs (keys_list) that I'm using to pull down sequence records using BioPython Entrez. I'd like to access just the sequence from fasta records returned, but I don't want to have to write the records to file to do so.
I'm trying the foloowing code
for key in key_list:
Entrez.email = "myemailaddress"
handle = Entrez.efetch(db='nuccore', id=key, rettype='fasta')
record = SeqIO.parse(handle, "fasta")
for seq_record in SeqIO.parse(record, "fasta"):
print seq_record.seq
When I run this I'm getting the error:
File "/usr/lib64/python2.6/site-packages/Bio/SeqIO/__init__.py", line 538, in parse
yield r
File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
self.gen.throw(type, value, traceback)
File "/usr/lib64/python2.6/site-packages/Bio/File.py", line 59, in as_handle
yield handleish
File "/usr/lib64/python2.6/site-packages/Bio/SeqIO/__init__.py", line 537, in parse
for r in i:
File "/usr/lib64/python2.6/site-packages/Bio/SeqIO/FastaIO.py", line 37, in FastaIterator
line = handle.readline()
AttributeError: 'generator' object has no attribute 'readline'
If I return the entire record with handle.read(), I can get the whole fasta record, but at this stage I'd just like to access the nucleotide sequence only.
Can anyone help me with this problem?
Many thanks in advance.
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:
'ggctcgcatctctccttcacgcgcccgccgccttacctgaggccgccatccacgccggttgagtcgcgttctgccgcctcccgcctgtggtgcctcctgaactacgtccgccgtctaggtaagtttagagctcaggtcgagaccgggcctttgtccggcgctcccttggagcctacctagactcagccggctctccacgctttgcctgaccctgcttgctcaactctacgtctttgtttcgttttctgttctgcgccgttacagatcgaaagttccacccctttccctttcattcacgactgactgccggcttggcccacggccaagtaccggcaactctgctggctcggagccagcgacagcccattctatagcactctccaggagagaaatttagtacacagttgggggctcgtccgggattcgagcgcccctttattccctaggcaatgggccaaatcttttcccgtagcgctagccctattccgcggccgccccgggggctggccgctcatcactggcttaacttcctccaggcggcatatcgcctagaacccggtccctccagttacgatttccaccagttaaaaaaatttcttaaaatagctttagaaacaccggtctggatctgccccattaactactccctcctagccagcctactcccaaaaggataccccggccgggtgaatgaaattttacacatactcatccaaacccaagcccagatcccgtcccgccccgcgccgccgccgccgtcatcctccacccacgaccccccggattctgacccacaaatcccccctccctatgttgagcctacagccccccaagtccttccagtcatgcacccacatggtgcccctcccaaccaccgcccatggcaaatgaaagacctacaggccattaagcaagaagtctcccaagcggcccctggaagcccccagtttatgcagaccatccggcttgcggtgcagcagtttgaccccactgccaaagacctccaagacctcctgcagtacctttgctcctccctcgtggcttccctccatcaccagcagctagatagccttatatcagaggccgaaactcgaggtattacaggttataaccccttagccggtcccctccgtgtccaagccaacaatccacaacaacaaggattaaggcgagaataccagcaactctggctcgccgccttcgccgccctgccagggagtgccaaagacccttcctgggcctctatcctccaaggcctggaggagccttaccacgccttcgtagaacgcctcaacatagctcttgacaatgggctgccagaaggcacgcccaaagaccccattttacgttccttagcctactctaatgcaaacaaagaatgccaaaaattactacaggcccgagggcacactaatagccctctaggagatatgttgcgggcttgtcaggcctggacccccaaagacaaaaccaaagtgttagttgtccagcctaaaaaaccccccccaaatcagccgtgcttccggtgcgggaaagcaggccactggagtcgggactgcactcagcctcgtcctccccctgggccatgccccctatgtcaagatccaactcactggaagcgagactgcccccgcctaaagcccactatcccagaaccagagccagaggaggatgccctcctattagatctccccgccgacatcccacacccaaaaaactccatagggggggaggtttaacctccccccccacattacagcaagtccttcctaaccaagacccaacatctattctgccagttataccgttagatcccgcccgtcggcccgtaattaaagcccagattgacacccagaccagccacccaaagactatcgaagctctactagatacaggagcagacatgacagtccttccgatagccttgttctcaagtaatactcccctcaaaaacacatccgtgttaggggcagggggccaaacccaagatcactttaagctcacctcccttcctgtgctaatacgcctccctttccggacgacgcctattgttttaacatcttgcctagttgataccaaaaacaactgggccatcataggtcgtgatgccttacaacaatgccaaggcgtcctgtacctccctgaggcaaaaaggccgcctgtaatcttgccaatacaggcgccagctgtccttgggctagaacacctcccaaggccccccgaaatcagccagttccctttaaaccagaacgcctccaggccttgcaacacttggtccggaaggccctggaggcaggccatatcgaaccctacaccgggccaggaaataacccagtattcccagttaaaaaagccaatggaacctggcgattcatccacgacctgcgggccactaactctctaaccatagatctctcatcatcttcccccgggccccctgacttgtccagcctgccaactacactagcccacttacaaactatagaccttaaagacgcctttttccaaatccccctacctaaacagttccagccctactttgctttcactgtcccacagcagtgtaactacggccccggcactagatacgcctggagagtactaccccaagggtttaaaaatagtcccaccctgttcgaaatgcagctggcccatatcctgcagcccattcggcaagccttcccccaatgcactattcttcagtacatggatgacattctcctggcaagcccctcccatgcggacctgcaactactctcagaggccacaatggcttccctaatctcccatgggttgcctgtgtccgaaaacaaaacccagcaaacccctggaacaattaagttcctagggcaaataatttcacctaatcacctcacttatgatgcagtccccaaggtacctatacggtcccgctgggcgctacctgaacttcaagccctacttggcgagattcagtgggtctccaaaggaactcctaccttacgccagccccttcacagtctctactgtgccttacaaaggcatactgatccccgagaccaaatatatttaaatccttctcaagttcaatcattagtgcagctgcggcaggccctgtcacagaactgccgcagtagactagtccaaaccctgcccctcctaggggctattatgctgaccctcactggcaccaccactgtggtgttccagtccaagcagcagtggccacttgtctggctacatgcccccctaccccacactagccagtgcccctgggggcagctacttgcctcagctgtgttattactcgacaaatacaccttgcaatcctatggactactctgccaaaccatacatcataacatctccacccaaaccttcaaccaattcattcaaacatctgaccaccccagtgttcctatcttactccaccacagtcaccgattcaaaaatttaggtgcccagactggagaactttggaacacttttcttaaaacaactgccccattggctcctgtgaaagcccttatgccagtgtttactctttcccctgtgatcataaacaccgccccttgcctgttttcagacggatccacctcccaggcagcctatattctctgggacaagcatatattgtcacaaagatcattcccccttccgccaccgcacaagtcggcccaacgggccgaacttctcggacttttgcatggcctctccagcgcccgttcgtggcgctgtctcaacatatttctagactccaagtatctttatcattaccttcggacccttgccctaggcaccttccaaggcaggtcctctcaggccccctttcaggccctcctgccccgcttactatcgcgtaaggtcgtctatttgcaccacgttcgcagccataccaatctacctgatcccatctccaggctcaacgctctcacagatgccctactaatcacccctgtcctgcagctctctcctgcagacctacacagtttcacccattgcggacagacggccctcacactgcaaggggcaaccacaactgaggcctccaatatcctgcgctcttgccacgcctgccgcaaaaataacccacaacatcagatgcctcaaggacacatccgccgtggcctactccctaaccacatctggcaaggcgacattacccatttcaaatataaaaatacactgtatcgccttcatgtatgggtagacaccttttcaggagccatctcagctacccaaaagagaaaagaaacaagctcagaagctatttcctctttgctccaggccattgcctatctaggcaagcctagctacataaacacagacaatggccctgcctatatttcccaagacttcctcaatatgtgtacctcccttgctattcgccatactacccatgtcccctacaatccaaccagctccggacttgtagaacgctctaatggcattcttaaaaccctattatataagtactttactgacaaacccgacctacctatggataatgctctatccatagccctatggacaatcaaccacctaaatgtattaaccaactgccacaaaacccgatggcagcttcaccactccccccgactccagccgatcccagagacacattccctcagcaataaacaaacccattggtattatttcaagcttcctggtcttaatagccgccagtggaaaggaccacaggaggctcttcaagaagctgccggcgctgctctcatcccggtaagcgctagttctgcccagtggatcccgtggaggctcctcaagcgagctgcatgcccaagacccgtcggaggccccgccgatcccaaagaaaaagaccaccaacaccatgggtaagtttctcgccactttgattttattcttccagttctgccccctcatcctcggtgattacagccccagctgctgtactctcacagttggagtctcctcataccactctaaaccctgcaatcctgcccagccagtttgttcatggaccctcgacctgctggccctt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