User: nameuser

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nameuser30
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Posts by nameuser

<prev • 10 results • page 1 of 1 • next >
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Calculating mutual information from FASTA files in Python
... I'm currently trying to write a program that will calculate Mutual Information given text files of nucleotide distributions. Below is the MI program, as seen I am currently stuck after finding marginal distribution, then dividing the values by the number of bins (8) in my Sort-Seq experiment: ...
fasta python pandas dataframe nucleotide written 7 weeks ago by nameuser30
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Mutual Information from Nucleotide Distribution in Python
... This question has been removed from this site -- please see stackoverflow if interested. --- #### Previous content restored by Ram from Google Cache --- Hi there, I'm currently trying to write a program that will calculate the mutation rate given text files of nucleotide distributions. I am hop ...
entropy written 11 weeks ago by nameuser30 • updated 7 weeks ago by _r_am32k
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Nucleotide Position Distribution Text File to Mutual Information - Python
... Hi there, I currently have a series of python programs that FASTA files are run through. At the end of the current work flow, the files are given an output displaying the distribution. Below is a short snippet of the A,T, G, C output 31 , 125066 , 77 , 38 84 , 59 , 35 , 125032 74 , ...
fasta python bash sequence mutualinformation written 11 weeks ago by nameuser30
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Comment: C: Changing output format for hamming distance of FASTA sequences (using Biopython)
... 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 5 months ago by nameuser30
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Comment: C: Changing output format for hamming distance of FASTA sequences (using Biopython)
... 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 5 months ago by nameuser30
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Comment: C: Changing output format for hamming distance of FASTA sequences (using Biopython)
... oops, must've missed that when I wrote the question. I just fixed their indentation! Thanks. ...
written 5 months ago by nameuser30
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Changing output format for hamming distance of FASTA sequences (using Biopython)
... 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. ...
fasta python hamming_distance biopython sequence written 5 months ago by nameuser30 • updated 5 months ago by Joe18k
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Comment: C: Counting mismatched characters from sequences from a fasta file in comparison to
... 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 6 months ago by nameuser30
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Comment: C: Counting mismatched characters from sequences from a fasta file in comparison to
... 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 6 months ago by nameuser30
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Counting mismatched characters from sequences from a fasta file in comparison to a reference sequence
... 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 ...
fasta python biopython written 6 months ago by nameuser30 • updated 6 months ago by Joe18k

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Student 7 weeks ago, asked a question with at least 3 up-votes. For Mutual Information from Nucleotide Distribution in Python

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