User: incensefrenzie2006

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Posts by incensefrenzie2006

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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 8 days 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 4 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 4 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 5 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 5 months ago by incensefrenzie20060 • updated 5 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 6 months ago by incensefrenzie20060 • updated 6 months ago by st.ph.n2.2k
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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 8 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 8 months ago by incensefrenzie20060
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Comment: C: Read In Multiple Text Files to Calculate a Threshold Python
... The updated answer seemed to do the trick! How could I transform the updated code into a function? ...
written 9 months ago by incensefrenzie20060
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Comment: C: Read In Multiple Text Files to Calculate a Threshold Python
... Thanks st.ph.n! My last question, if I write another function to check e value, how can I append the first two columns with the e value. My last step: if eval is less than threshold: # append fields [0], [1],[10] print NP_387917.1 ADZ06570.1 7e-77 ...
written 9 months ago by incensefrenzie20060

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