Genskew_cc is the commandline client (therefore the _cc) for GenSkew. It is tested on all major operating systems (Linux, Windows, Apple) and installable via the pypi page.
Upon opening the terminal or command prompt, the following command will bring up a description of the usage:
$ python3 -m genskew -h
There is one positional argument: the filelocation. This can be a direct path, a path to a folder with Fasta, Genbank or the respective gz files in it or multiple paths seperated by a space.
Optional arguments are marked with a - before it. Besides -h there are 7 optional arguments:
1. -s [stepsize]
This argument sets the stepsize. If it is not used the stepsize is calculated by dividing the length of the sequence by 1000.The step and windowsize are limited to 100. This is because if they are lower, there could be none of the specified nucleotides in the window and the formula used to calculate the skew would divide by 0.s
2. -w [windowsize]
This argument work just like the stepsize, but sets the wndowsize.
3. -o [outfiletype]
This argument sets the output filetype in which the graph is saved. The default is png, but there are many options to choose from. In the help text which you see when using -h you can find a list of supported filetypes.
4. -n1 [A, C, G or T] and -n2 [A, C, G or T]
With these two arguments you can specify the first and second nucleotide. The default is G and C.
5. -d [dpi]
This argument sets the dpi that your graph is going to be saved with.
6. -of [outputfolder]
This argument sets the folder that the graphs are going to be saved in. The default saves them to wherever the sequence files where.
7. -sk [skewIT]
This argument changes from the GenSkew graph algorithm to the SkewIT¹ algorithm.
1: SkewIT, https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008439 (06.04.2022), SkewIT: The Skew Index Test for large scale GC Skew analysis of bacterial genomes, Jennifer Lu, Steven L. Salzberg