User: incensefrenzie2006

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Posts by incensefrenzie2006

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Create Seq Record(s) Object from my SORTED list!
... It was enumerate was incorrect... import re, glob, sys from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.Alphabet import IUPAC # Create a file path for glob function path = '/Users/sueparks/' + 'P_*' + '_FASTA. ...
written 11 weeks ago by incensefrenzie20060
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Create Seq Record(s) Object from my SORTED list!
... I have a program that reads in ~20 fasta files, then I parse the id name and sequence name. This information is then appended to a list and sorted...I am sorting on the first element, the directory/filename. (Next I will concatenate all of the similar sequences, so I would like to use Biopython) H ...
python biopython seq record written 11 weeks ago by incensefrenzie20060
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Comment: C: Is There A Way To Skip Existing Keys In Seq.Io.To_Dict? Or Is There A Better Way
... How would the schematics of the code change if James had multiple files? For example, NC_000913.faa thru NC_000923.faa. ...
written 3 months ago by incensefrenzie20060
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Comment: C: Master dictionary of database file (2D dictionary) using Biopython, then specify
... I was thinking about the glob function, but maybe there is an easier method path = '/Users/sueparks/' + 'P_*' + '_Results.txt' for file in glob.glob(path): with open(file, 'r') as f: line = f.readlines() print line ...
written 7 months ago by incensefrenzie20060
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Comment: C: Master dictionary of database file (2D dictionary) using Biopython, then specify
... the re module is very useful in this case. Now I am curious how to iterates through my results files, which is basically a handful of text files, with one column of data. How could I iterate through these files and check my master dictionary?? EEQ68960.1 EEQ26037.1 EFE00375.1 ...
written 7 months ago by incensefrenzie20060
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Comment: A: Master dictionary of database file (2D dictionary) using Biopython, then specify
... Hello, I know have a for loop that seems to work fasta_files = "L_214.txt","L_224-1.txt" # two files that are used as my database(s) recs = [rec for f in fasta_files for rec in SeqIO.parse(f, 'fasta')] print recs Output: id='EFB61523.1', name='EFB61523.1', description='EFB6152 ...
written 8 months ago by incensefrenzie20060
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Master dictionary of database file (2D dictionary) using Biopython, then specify key with string
... My goal is to create a 2d dictionary, search for some sequence ids, and then writes the organism name with the amino acid sequence to a file I have a working code that creates one dictionary, and looks for the id numbers that I want, and writes it to a file. I am unable to iterate through all my ...
fasta python dictionary written 8 months ago by incensefrenzie20060 • updated 8 months ago by cindy.perscheid90
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Write List of subject ID numbers to a new text file(s)
... I have a function that can read in the first line of multiple blastp files. I use a for loop to iterate through the files and print the subject ID numbers from the first line of each file. How could I write each list to its own file?? import os, glob, sys #This method reads in column ...
python subject id number written 9 months ago by incensefrenzie20060 • updated 9 months ago by st.ph.n2.3k
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Comment: A: Convert a FASTA Amino Acid Sequence to RNA (Reverse Central Dogma)
... I was under the impression that Biopython had method(s) to work this kind of problem, but I was not considering the "redundancy" of the codon table. ...
written 11 months ago by incensefrenzie20060
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Convert a FASTA Amino Acid Sequence to RNA (Reverse Central Dogma)
... I see lots of example on how to convert DNA to RNA or RNA to Amino. I see plenty examples using Python and Biopython. How could I do the reverse? Amino acid sequence to RNA and then RNA to DNA. #### Define a dict that maps Amino acids to the corresponding codon AA_codon = { 'C': ['TGT ...
python sequence written 11 months ago by incensefrenzie20060

Latest awards to incensefrenzie2006

Scholar 11 weeks ago, created an answer that has been accepted. For A: Create Seq Record(s) Object from my SORTED list!

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