pythonscript to find the number of homologous genegroups within a genome.

[Arif Mahmud]

Dear all, please kindly help me to
solve this problem by python script
writing. I am a beginner in script
writing.
Problem: A homologous gene group
consists of genes, which have an
alignment to at least one other gene
in the group with both a % sequence
coverage and % identity equal to or higher than a
given stringency cutoff. Write a python program
to find the number of homologous gene groups
within a genome at various levels of stringency.
For example with a stringency of 10, every gene
in a group should have a % sequence coverage
and % identity of at least 10% with at least one
other gene in the group. The program should take
a single genome file in genbank format on the
command line and write a csv file called
"output.csv" in the directory. The ouput file
should consist of 10 lines, each line should have
the stringency used (0 to 100, in increments of
10) and the number of homology groups. (See
example below). write the python program as a
txt file.
Example: 0,13456 10,234 20,234 30,200 40,190
50,187 60,187 70,100 80,95 90,55 100,45

[rhinoceros]

That's quite hardcore homework you have there, especially if you're supposed to do it from scratch

[Arif Mahmud]

yes its a hardcore one but have to solve it. I need all of your help. As I am a beginner in programing language from a biological background have no idea what to do. something good is depend on it. please kindly help me.

[rhinoceros]

yes its a hardcore one but have to solve it. I need all of your help. As I am a beginner in programing language from a biological background have no idea what to do. something good is depend on it. please kindly help me.

Drop out and take a class that is more to your level? Beginners should be doing hello worlds and such. Not this. Are you allowed to use other programs in your script or are you supposed to implement multiple sequence alignment etc. from scratch?

[Arif Mahmud]

its a requirement. if I solved this problem my application process will be further proceed. only python script will be allowed. yes I think about implementation of multiple sequence alignment

[rhinoceros]

Well, I wouldn't know how to implement such things from scratch. It seems to me like you're applying to the wrong place. I wouldn't apply to say some physics grad school with my high school physics only background. Anyway, good luck. I doubt anyone here will help you 'cheat' your way through this, but who knows..