checking for overlapping

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checking for overlapping

Postby betty3 » Tue May 07, 2013 9:22 pm

I am new to programming. I need to write program in python which do following:
Read the lines of the file where in each line there are 4 colums:
1st one is a name of protein,
the second one is a name of domain in the protein(the building block of protein, as protein can be created by several domain),
the third one is a start location of the domain(number) in the protein and
the fourth one is a end location (number) of the domain in the protein.
I need to check if domains in the same protein ( so for the same id in colum 1) overlap. The rule is: two domains overlap if more then 10% of of the predicted
domain locations were overlapping (based on the relative length of the
Can you help me to write this code please.
Many thanks
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Re: checking for overlapping

Postby micseydel » Tue May 07, 2013 10:43 pm

I will read your post once you've read this.
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Re: checking for overlapping

Postby betty3 » Wed May 08, 2013 5:34 am

I know the python syntax but really straggled with this task. I don't really know how to translate into the language the overlapping situation. Do I need to use a set ranges for it.
I must underline that this is not a homework. I just need help if you can help me.
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Re: checking for overlapping

Postby Mekire » Wed May 08, 2013 5:51 am

Regardless of whether it is homework or not, we generally like to see some sort of attempt (posted correctly in code tags) before assisting. We have no clue what you do or do not know how to do. Do you know how to extract the data from your files? Do you know how to compare the domains?

Post an attempt, be it bad or good. Tell us what error it is giving or how the result is differing from what you want.

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