User: nameuser
nameuser • 10
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Posts by nameuser
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... if __name__ == '__main__':
with open(filename + "out.fasta", "w") as f:
for record in (SeqIO.parse(filename, 'fasta')):
if hamming_distance(str(record.seq)) < 50 :
print(">{id}\n{seq}".format(id=record.id, seq=record.seq), file=f)
...
written 10 days ago by
nameuser • 10
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... The logic definitely makes sense to me, I adjusted it a little for errors but the print line was extremely helpful! I'm getting a blank output right now though, when I did a matrix for the sequences, there were plenty (500,000 sequences per file) with less than 50. Additionally, dh is being defined. ...
written 11 days ago by
nameuser • 10
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... oops, must've missed that when I wrote the question. I just fixed their indentation! Thanks. ...
written 11 days ago by
nameuser • 10
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... Hi there,
I currently have the code stated below. The output I currently have it set to write out is not what I'm looking for. However, this has been the only way I have successfully run the script. I would like to remove the sequences from a fasta file that have a hamming distance of 50 or more. ...
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... from Bio import SeqIO
import sys
file = SeqIO.parse("file.fasta", "fasta")
def hamming_distance(s1, s2):
if len(s1) != len(s2):
raise ValueError("ALIGN!")
return sum(ch1 != ch2 for ch1, ch2 in zip(s1, s2))
result = []
for i, record in enumer ...
written 21 days ago by
nameuser • 10
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... I tried to add another if statement to remove the sequences with a hamming distance >50 but I was unable to write that in the file, any suggestions for outputing a new fasta file removing those with a count over 50? ...
written 22 days ago by
nameuser • 10
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... I am attempting to use Biopython to compare all the sequences (~400,000) to a reference sequence. I parsed the fasta file using: for record in SeqIO.parse("filename.fasta", "fasta").
Can someone help with the code to loop over the sequencing in the fasta file and compare it with a string, the refe ...
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