4. Operation command of TGFam-Finder > Manual

4.1.2. Construction of output directories in the running folder

Build_TGFam-Finder.pl firstly checks whether users correctly configure information of programs in PROGRAM_PATH.config and resources in RESOURCE.config. If users omits or inaccurately input the information, Build_TGFam-Finder.pl generates messages for detailed errors. Build_TGFam-Finder.pl secondly confirms whether output directories in PROGRAM_PATH.config are already existed in running path. If there are directories having the same name of output folders, users should delete or rename the directories. Finally, Build_TGFam-Finder.pl creates output directories under running path that users input in PROGRAM_PATH.config if no errors are discovered.
Usage:

$perl Build_TGFam-Finder.pl absolute_path_containing_config_files RESOURCE.config PROGRAM_PATH.config
(ex. $perl /home/TGFam-Finder/TGFam/scripts/Build_TGFam-Finder.pl /home/TGFam-Finder/TGFam/test_sample PROGRAM_PATH_test.config RESOURCE_test.config)

After running Build-TGFam-Finder.pl, Run_TGFam-Finder.sh, a script that runs TGFam-Finder, is automatically created.

Note that you must use the ‘. (dot)’ when using the shell command.

$. Run_TGFam-Finder.sh
(ex. $. Run_TGFam-Finder.sh)

4.3. Final outputs of TGFam-Finder

Final gene models including gff3, peptides, coding DNA sequences and tsv files are generated

Usage:
$cd Final_directory && ls

(ex. $cd /home/TGFam-Finder/TGFam/test_sample/Final && ls)

Usage:
$cat Prefix.TGFam.CDS.fa

Usage:
$cat Prefix.TGFam.gff3

Usage:
$cat Prefix.TGFam.PEP.fa

Usage:
$cat Prefix.TGFam.PEP.fa.nostop.tsv