PersephoneShell provides simple directory browsing functions. They enable listing files and directories and navigating throughout the file system. For example, to minimize typing, you can change current directory (cd) to the folder with the INI files of a certain category and then reference the control files by name, without providing the full path:

PS> cd Samples/Sequence
PS> add sequence -c Wm82.a4-phytozome.ini -t

The file listing function (ls) shows the contents of the current directory. For example, the output of the command for a data folder would look like this:

PS> ls
Yinping-Jiao-2016-Study.vcf.gz
sorghum_bicolorv5_core_6_87_5.gff.gz
Sorghum_bicolorv5.Sb-BTX623-REFERENCE-JGI-5.1.dna_sm.toplevel.fa.gz

The format of the listing can be changed by using the switch -l (long listing) or -n (long listing with numbers in plain format):

PS> ls -l
Directory contents of /data/Data/sorghum

Name                                                                                Size
------------------------------------------------------------------------------------------
Yinping-Jiao-2016-Study.vcf.gz                                                     1.56 GB
sorghum_bicolorv5_core_6_87_5.gff.gz                                               7.68 MB
Sorghum_bicolorv5.Sb-BTX623-REFERENCE-JGI-5.1.dna_sm.toplevel.fa.gz              202.18 MB

Sometimes, it is easier to read the file sizes using a plain numbers like this:

PS> ls -n
Directory contents of F:\data\sorghum

Name                                                                            Size (B)
------------------------------------------------------------------------------------------
Yinping-Jiao-2016-Study.vcf.gz                                               1,671,944,354
sorghum_bicolorv5_core_6_87_5.gff.gz                                             8,050,308
Sorghum_bicolorv5.Sb-BTX623-REFERENCE-JGI-5.1.dna_sm.toplevel.fa.gz            212,004,201

To print the current working directory, use the command pwd:

PS> pwd
Current directory: /data/Data/sorghum