Working with sam file as a table

[Lilach1234]

Hey all,

I am working with a sam file and i want edit it and manipulate it as a normal table. there are few limited options in galaxy but it takes forever in queue and I want a more freedom. Is there any free program similar to excel or something sql based i can upload my file to and treat it like a normal table?
Any pointer will be highly appreciated
Thanks in advanced

[swbarnes2]

Sam files are millions of lines long. I think you need to rethink what you are doing. Editing a file like that manually is almost certainly not the right way to do whatever you want to do. You should either pull out a smaller subset of reads to examine, or use a script to go through all the lines for you.

[Lilach1234]

Thank you for your answer, I guess i wasn't clear enough i wanna query the sam file by addressing it as a table, like i would have done if i could upload it to mysql server and query it using sql tools or BI tools like oracle.
If not how can i manipulate the data, even if it will be working on a smaller subset?

[dpryan]

Assuming the file is coordinate sorted, you can simply "samtools view file.bam region" to get reads over a region. If you need things done more programatically, there are APIs that yield direct access. The C API is described on the samtools webpage on sourceforge and I find it pretty convenient. There's likely to be a similar API for whatever language you normally prefer.