Looking for Tutor (computer science)

b00mIR

Hi

I'm a master's student in biotechnology, looking for someone who could help me work with MS DOS and Linux command lines and also make batch files and Linux executables. Also any experience in programming with Perl or python would be helpful but not necassary. This would be in order to help me with my research project which is genomics based

Send me a pm if you're interested

cheers

bnt

There's not much to it, really. A batch file on Windows is basically a text file with a list of commands in it, and you save it to any handy location e.g. the Desktop and run it from there.

There are various things you can do in a batch file to make your life easier. Examples:
- if you've saved the PLINK program to a directory, you can create an "environment variable" using the SET command to make access to it quicker. It helps keep command lines shorter and easier to understand;
- If you have a bunch of data files, you can use a FOR command to work on each of them in order - by number or by "wildcard" (e.g. *.DAT).
- REM commands are comments - use them to describe what you are doing, so you can come back later and understand what you did;

You could end up with something like this in the batch file:

REM set variable with %PLINK% program location 
SET PLINK=C:\PLINK\PLINK.EXE

REM navigate to the data directory e.g. H:\DATA
H:
CD H:\DATA

REM data files are named OUT12 through OUT20: run PLINK on them all
FOR /L %%n in (12,1,20) DO %PLINK% --ped OUT%%n.ped --map MAP%%n.map 

Wherever you see %%n, after DO, it would be replaced by a number from 12 to 20 inclusive i.e. it would loop %%n from 12 to 20. There's a good reference to FOR and other DOS commands on the Microsoft website here. I haven't tested this batch file, obviously, but if you can learn to use FOR ... DO, that's one of the key ways of automating lots of work in MS-DOS batch files.

UNIX scripts are almost the same - the makers of MS-DOS borrowed methods from early UNIX anyway - but the syntax is slightly different e.g. they'll use $ signs instead of %% to reference variables. I saw in the other thread you opened that you've tried using it under Cygwin. I wouldn't bother with that kind of thing unless I gained some major advantage from doing so - and I don't see anything to gain in this case. It's the same program, and they already provide a MS-DOS version which does the same job. It is educational, though. I've done a bit of that, and a bit of Python, but I do not like Perl at all.

I'm not in CompSci, I've just been doing this stuff for years. I'm on campus regularly and could come to your lab if that would help.

b00mIR

Wow thanks for the help, i'll see how i get on with it now and let you know. Again thanks, very much appreciated

meemeep

also - try these guys:

http://www.csi.ucd.ie/content/computer-science-support-centre