Project 1
Project 1 is now available in pdf here. The project data can be found archived here (and in zip format). You can also get the project and all the project data simply by pulling from the class git repository; the project files are in the c260/2009 subdirectory. If you’ve already cloned the git repository:
git pull origin master
Or to clone the repository for the first time:
git clone http://www.doe-mbi.ucla.edu/~leec/c260.git
An example of the contents of the makefile using the example “reader.c” as the source code is:
gcc -o vfinder reader.c
For simple programs that do not depend on other libraries it is of the format:
gcc -o
If you use the math library, you might need to include the “-lm” flag in the above command.
Do we have a recommended value for the number of subdivisions in the integration?
I would recommend at least 100 values. Try a few values (100, 150, 200, 500, …) and see if your results differ significantly (they should converge).
Could you please show us how to write the vfinder file if we are using python?(assume the scripts name is “reader.py”)
the content of vfinder should be:
Should our scrpits read from stdin or from files?
Read from the standard input stream.
Dear nils，
I guess you will use pipe to push input in our programs.
Do you know how can we test that on Window python shell?(Is there a pipe?)
I am not too familiar with the Window shell. Try some googling to figure it out. For example, here’s a link that may be of some use. It looks like piping is possible on the windows shell.
just so you know you can also use
vfinder < input.txt (instead of piping)
(and yes the normal pipe works in windows, you just might need a program to pipe it from)
I’m having some problems with the sample program. I found that DBL_MIN is the smallest absolute value capable of being represented by a double, not the most negative number. I used -HUGE_VAL instead.
Here are the expected values for the scores, as given by the last class’s TA. This can be found in comment 35 in last year’s post for project 1. I’m not sure how much, if anything, has changed from the last project.
http://c260a.bioinformatics.ucla.edu/2008/10/09/project-1/#comments
Ran into this problem with Python 2.5:
float(”-inf”) - float(”-inf”) = nan, when it’s expected to be 0.
This messed up my AVSM scores.
The spec says to have a file named “make” which is used to compile the program. Is that supposed to say “Makefile” or “make”? If it’s make, does that mean we write a shell script which calls gcc or g++?