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CCGG26
CCGG26
Joined: Sep 17 '10
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  • CCGG26
    replied to need help with substring alignment
    in this situation the ---TGT--- needs to be read as is...we cannot ignore the dashes or the program will not work
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  • CCGG26
    replied to need help with substring alignment
    ok, i inserted this into the program but nothing printed and there wasnt an error message

    Code:
    filename = input("Please enter a filename:")
    with open(filename, "r") as myfile:
        data = myfile.readlines()
    for i in range(len(data)):
        data[i] = data[i].rstrip("\n")
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  • CCGG26
    replied to need help with substring alignment
    ok, by any chance is it possible to make this read from a txt file and for it to work for any substring alignment
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  • CCGG26
    started a topic need help with substring alignment

    need help with substring alignment

    Situation..Give n two sequences, where one is a substring of the other, we define a substring alignment by matching the substring with the longer sequence and placing gaps everywhere else. For example if the input is ACCTGTAGG and TGT then the substring alignment is

    ACCTGTAGG
    ---TGT---

    i need help designing program that prints the substring alignment of two unaligned sequences. If no substring alignment exists...
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  • CCGG26
    replied to How to get the number of A's in each column?
    great, can this way work for any sequence or just this specific problem...if the sequences were of any length how would you combine them without having to type out each sequence?
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  • CCGG26
    replied to How to get the number of A's in each column?
    ok, im having trouble understanding zip(*sequences) ..ive never used that before at my level of programming and was wondering if there is an alternative method
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  • CCGG26
    replied to How to get the number of A's in each column?
    Code:
    with open("e:/dna14.txt", "r") as myfile:
        data = myfile.readlines()
        myfile.close()
        
    for i in range(0, len(data), 1):
        data[i] = data[i].rstrip("/n")
    
    column_number = input("Please enter a coumn number: ")
    column_number = int(column_number)
    
    ch1 = (data[1])[column_number]
    Acount = 0
    See more | Go to post
    Last edited by bvdet; Nov 18 '10, 11:01 PM. Reason: Please use code tags when posting code. [code]....code goes here....[/code]

    Leave a comment:


  • CCGG26
    started a topic How to get the number of A's in each column?

    How to get the number of A's in each column?

    ...hey guys.. how can you write aprogram that prints the number of A's in each column of a multiple sequence alignment. For example for the multiple alignment below

    >human
    ACCT
    >mouse
    ACCT
    >cat
    TCCT
    >dog
    ACAT

    the output should be

    2 0 1 0
    See more | Go to post

  • CCGG26
    replied to Print column numbers that are 100% conserved
    A 100% conserved column is
    one that has the exact same nucleotide in every sequence. For example if the
    user enters 1 and the the multiple alignment below is given as input

    >human
    ACC
    >mouse
    ACC
    >cat
    TCC
    >dog
    ACA

    then the output should be "No". But if the user enters 2 then the output
    should be "Yes".
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  • CCGG26
    replied to Print column numbers that are 100% conserved
    output: column 2 = 100%
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  • CCGG26
    replied to Print column numbers that are 100% conserved
    the fasta format multiple alignment is just a name i believe, i do not think it is anything significant..
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  • CCGG26
    started a topic Print column numbers that are 100% conserved

    Print column numbers that are 100% conserved

    how can i write a Python program that prints the column numbers in a FASTA format multiple alignment that are 100% conserved. im really having trouble getting a grip of this concept...For example in the multiple alignment below

    >human
    ACC
    >mouse
    ACC
    >cat
    TCC
    >dog
    ACA

    column 2 is 100% conserved but columns 1 and 3 are not 100% conserved.
    See more | Go to post
    Last edited by bvdet; Nov 12 '10, 02:13 AM. Reason: Remove question from title

  • CCGG26
    started a topic how can i shorten this program??

    how can i shorten this program??

    Code:
    map = {}
    dna = [ "A", "C", "G", "T"]
    
    with open("matrix.txt", "r") as myfile:
        line = myfile.readline()
        mylist = line.split()
        map{"AA"} = mylist[0]
        map{"AC"} = mylist[1]
        map{"AG"} = mylist[2]
        map{"AT"} = mylist[3]
        line = myfile.readline()
        mylist
    ...
    See more | Go to post
    Last edited by bvdet; Nov 10 '10, 02:41 AM. Reason: Add code tags [code]....code goes here....[/code]
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