Problem 1
Let say I have a file name peaks.txt.
Chr1 7 9 4.5 5.5
chr10 6 9 3.5 4.5
chr1 10 6 2.5 4.4
Question is how can i sort the file so that it looks like this:
Chr1 7 9 4.5 5.5
chr1 10 6 2.5 4.4
chr10 6 9 3.5 4.5
Next is how do I extract out the p-values(i.e. 7,9,10,6,6,9)
After I extracted out all the p-values. for example all the p-values from chr1 is 6,7,9,10 and for chr10 are 6 and 9.
So for example if the p-value is 7 from chr1, i would open out a file called [login to view URL] which look like this:
>chr1
ATTGTACT
ATTTGTAT
ATTCGTCA
and I will extract out the subsequence TACTA. Basically p-value(in this case its 7) position counting from second line of the [login to view URL] file and print out the subsequence from starting from position 7-d and 7+d, where d=2. Thus if the p-values is taken from chr10 then we read from the a file with file name [login to view URL] which can look like like:
chr10
TTAGTACT
GTACTAGT
ACGTATTT
So the question is how do I do this for all the p-values.(i.e all the p-values from chr1 and all the p-values from chr10) if let say we dont know [login to view URL] files have how many lines.
And how do i output it to a file such that it will have the following format:
Chr1
peak value 6: TTGTA
peak value 7: TACTA
etc etc for all the p-values of chr1
chr10
peak value 7: TTACT
etc etc etc...
Problem 2, after generating the result, I wanna look for the number AGAACA or TGTTCT in the each sequences generated by each p-values. Plot an histogram with interval of together with the line graph. if d=2 then the x-axis is -2 to 2. So some conversion of values is need.
Take note I am working with bioinformatics so I hope you all can make use of numpy.
Note the above 2 problems are for Python.
The following problem are for microsoft access.
How do I port the output of a query straight away to an existing excel file. The data must be added to a specific starting cell.
Take note bidder need not bid for all the problems. However, Problem 1 and 2 are to be bid together. while problem 3 can be bid separately.
Thanks.
Deadline is next week since its just a simple project.
Dear Client,
I am much familiar with Python programming related with bioinformatics and can help you out. Please get back to me as soon as possible if you need my help.
With Regards,
Koustav
Hi Sir, We are bidding for all 3 bids. And we need more information about the third bid.
I am a python programmer and the leader of our python developing team. Our team consists of several programmmers with expertise and rich experience in Python.
The python programs We designed are elegant and scalable. We are convinced to help you finish this project in high quality and efficiency. We all cheish this opportunity. Welcome to contact us. Thank you.
Hi, unfortunately I'm flying until Monday but I could do the project that evening. I used to work in bioinformatics -- before greener pastures called. Anyway this is a simple enough job (I'm bidding on Problems 1 and 2, I haven't the faintest clue about Access).
By the way, you won't need numpy for the simple kind of manipulation you describe.
Cheers,
laddie
Hello, I have a lot of experience in python scripting and data manipulation. I can deliver you with the highest code quality and testing. I am interested to do problem 1 and problem 2.
Regards
Hi
I have a MS in Bioinformatics with 6+ years experience using Perl, BioPerl, BioJava, and PHP to develop and implement life sciences solutions for genomics and proteomics. My focus on this project was on gene prediction.
This experience is a perfect overlap with the requirements of your project
I believe I can complete the project and provide an usable and accurate solution in the specified time and would appreciate if you consider my bid favorably.
I am experienced developer of bioinformatics software, though my previous work has been with MATLAB, I am well acquainted with Python and can certainly solve the specifically problems presented here in a clean, easily understandable and readable way.