Consider I get 10 files of size 3 GB every week, which I am supposed to filter based on certain column using a reference index and forward to my colleague. Before filtering I also want to check how the file looks like: column names, first few records etc.
I can use something like following to explore few rows and few columns.
$$ awk '{print $1,$3,$5}' file | head -10
And then I can use something like sed with reference index to filter the file. Since I plan to repeat this with different files, databases would be time consuming(even if I automate it loading every file and querying). Due to the file size options like R, Python would be slower than unix commands. I can also save set of commands as script and share/run whenever I need it.
If there is a better way I would be happy to learn.
When you have to deal with (genetic data) files of few GB on daily basis, I dont think using Python, R or databases is good idea to do basic data exploring.
I can use something like following to explore few rows and few columns. $$ awk '{print $1,$3,$5}' file | head -10
And then I can use something like sed with reference index to filter the file. Since I plan to repeat this with different files, databases would be time consuming(even if I automate it loading every file and querying). Due to the file size options like R, Python would be slower than unix commands. I can also save set of commands as script and share/run whenever I need it.
If there is a better way I would be happy to learn.