User: incensefrenzie2006

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Posts by incensefrenzie2006

<prev • 10 results • page 1 of 1 • next >
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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 3 days 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 4 days ago by incensefrenzie20060 • updated 3 days ago by cindy.perscheid80
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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 4 weeks ago by incensefrenzie20060 • updated 4 weeks ago by st.ph.n1.9k
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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 weeks 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 weeks 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 4 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 4 months ago by incensefrenzie20060
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Answer: A: Read In Multiple Text Files to Calculate a Threshold Python
... You are correct, I did not upload the entire code. I have a separate function for the threshold (the median calculation). import subprocess, sys, math def median(a): a.sort() if len(a)%2!=0: median=a[len(a)/2] else: median=(float(a[len(a)/2]+a[(len(a)/2)- ...
written 4 months ago by incensefrenzie20060
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Comment: C: Read In Multiple Text Files to Calculate a Threshold Python
... This is very useful.... I was trying to work with the glob module, but I initially thought it would be best to combine ALL my files into one text file, then sort, then return the e-value...but that was not working properly. import glob list_files = [] for file in glob.glob('/Users/sue ...
written 4 months ago by incensefrenzie20060
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Read In Multiple Text Files to Calculate a Threshold Python
... I have ~ 400 text files of BLASTp results. P_1L_GRL111.out (contents) NP_387917.1 ADZ06570.1 44.29 289 153 4 2 289 1 282 7e-77 236 I have a file that reads in files ALL my P_1 files, sorts the e values, and then calculates a threshold. I would like to convert this into a function ...
python e-value written 4 months ago by incensefrenzie20060

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