The gausssort utility was designed to read in output files of the following format:
#Tick Number: 0 #A_bacteria #B_bacteria #_bacteria
1 9 20 29
2 11 21 32
3 11 30 41
4 11 39 50
5 13 48 61
6 16 65 81
7 18 80 98
8 21 102 123
9 25 134 159
...
Specifically, this includes four entries separated by ' ' characters (i.e space characters). It is NOT currently generalized to work with other file types.
For each file it finds in the given path (see Usage section) it will read in the data, and calculate the standard deviation for that series of data. Once it has completed reading all the files it will return a list of file names sorted in ascending order by standard deviation.
Installing the utility from the command line is simple, follow these steps:
cd <location_you_want_to_clone_to>
git clone https://github.com/RagingTiger/GaussianSort.git
Or if you would prefer to simply download the repository as a zip file:
Simply click on the 'green' Clone or download button.
Currently the utility is not setup to be installed as a global utility. To use it you must first 'cd' into the GaussSort directory:
cd GaussSort/
Once in the directory GaussSort the utility is simple to use, but there are several options to be aware of:
Usage:
gausssort bact.a <read_file_path> [save [<write_file_path>]]
gausssort bact.b <read_file_path> [save [<write_file_path>]]
gausssort bact.total <read_file_path> [save [<write_file_path>]]
First, to clarify, the above usage statement is written in the docopt syntax and it is more simple than it appears. The first word gausssort can be ignored, only the other four words need to be considered. The first of these words is a subcommand specifying which column of data (i.e. #A_bacteria, #B_bacteria, #_bacteria stored in each file shown in the Description section) to calculate the standard deviation on:
bact.a
bact.b
bact.total
The next word '<read_file_path>' will be the path to the files you want to sort. For example, if I wanted to launch the utility and sort on the '#A_bacteria' data in each of the files located in the '/home/gauss/data' directory:
./gausssort.py bact.a /home/gauss/data
This usage will print to stdout the file names sorted with their 'gaussian widths' (i.e. standard deviation) next to each name:
1: test-A_0_0.2_0.5_0.5_0.5_0.5.dat 2.62489899361
2: test-A_0_0.4_0.5_0.5_0.5_0.5.dat 2.62489899361
3: test-A_0_0.6_0.5_0.5_0.5_0.5.dat 2.62489899361
4: test-A_0_0.8_0.5_0.5_0.5_0.5.dat 2.62489899361
5: test-A_0_0_0.5_0.5_0.5_0.5.dat 2.62489899361
6: test-A_0_1_0.5_0.5_0.5_0.5.dat 2.62489899361
7: test-A_0.2_0.2_0.5_0.5_0.5_0.5.dat 3.03493910298
8: test-A_0.2_0.4_0.5_0.5_0.5_0.5.dat 3.03493910298
9: test-A_0.2_0.6_0.5_0.5_0.5_0.5.dat 3.03493910298
10: test-A_0.2_0.8_0.5_0.5_0.5_0.5.dat 3.03493910298
...
A more advanced usage involves the save command:
./gausssort.py bact.a /home/gauss/data save
This will run the utility and write the output to a file in the GaussSort directory. The output file will be named based on the date and time, and will therefore be a unique file and not in danger of being overwritten.
Optionally, you can give a name to the output file:
./gausssort.py bact.a /home/gauss/data save list_of_gausssorted_filenames.txt
This will of course save the output in the 'list_of_gausssorted_filenames.txt' file.