[BioPython] How to access the actual sequence from Bio.SeqIO.FASTA
Wijaya Edward
ewijaya at i2r.a-star.edu.sg
Tue Oct 3 06:34:09 UTC 2006
Dear experts,
I have the following script which try to
use Bio.SeqIO's FASTA method to read
sequence and simply print the actual sequence.
__BEGIN__
from Bio.SeqIO import FASTA
import sys
handle = open(sys.argv[1])
it = FASTA.FastaReader(handle)
seq = it.next()
while seq:
print seq.seq
seq = it.next()
handle.close()
__END__
But how come the output looks like this?
Seq('AACTAACAGTTTCCCTTGTCTAAAGCCTGCTCCCGATAAAAATAAGGCTGTGGGTTCTGG ...', Alphabet())
Seq('CACCATCAGGGCGAGATTTAGCCGCTAGGTTTGTCTCATGGAAGAAAAGCAGTAGAAAAA ...', Alphabet())
Seq('ACTTCCCACGTACGTCTGCAGGAACTTGCCTGTACCACAGGAAGACGATCGTCATGAGAA ...', Alphabet())
Is there a way to get the actual plain ATCG sequence (i.e wihtout brackets,quotes,and Alphabet()).
Sorry I'm new with Python. Please bear with me.
Thanks and hope to hear from you again.
Regards,
Edward WIJAYA
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