#Warning on proper execution of SecNet: ####################################### Please launch SecNet as an executable, i.e. ./secnet.py3; do NOT try to execute secnet.py3 with your own python, for example please AVOID "/bin/python secnet.py3". Your python may not include required libraries. Please execute secnet.py3 as executable, i.e. ./secnet.py3; for the proper execution the first line of secnet.py3 includes a reference to Anaconda Python 3 locally installed to the SecNet kit directory. #Example: ######### #To predict secondary structure of a single sequence with the 8-label DSSP alphabet: ./secnet.py3 --input input/example.fasta --output output/ --label 8 #Other examples: ################ #Please note you need to use double or single quotes around wildcard characters such as '*.seq' or '*.fasta": ./secnet.py3 --input "input/*.fasta" --output output/ --label 8 #If you wish to process all testing entries in Test2018: ./secnet.py3 --input Test2018/input --output Test2018/output --label 3 --rule 1 #To generate all available label sets: {8 labels, 5 labels, 4 labels and 3 labels of both Rule #1 and Rule #2): ./secnet.py3 --input input/5UB3B.fasta --output output/ --label all #4 labels only: ./secnet.py3 --input input/5UB3B.fasta --output output/ --label 4 #5 labels only: ./secnet.py3 --input input/5UB3B.fasta --output output/ --label 5 #The easier 3 labels of Rule #2: ./secnet.py3 --input input/5UB3B.fasta --output output/ --label 3 --rule 2 #To limit CPU usage to a single core with longer execution time (by default all CPU cores are used): ./secnet.py3 --input "input/*.fasta" --output output/ --label 8 --cpu 1 #If you have 8 cores, you may limit to 4 cores: ./secnet.py3 --input "input/*.fasta" --output output/ --label 8 --cpu 4 #To reduce amount of standard output and only report whether each sequence was successfully processed: ./secnet.py3 --input "input/*.fasta" --output output/ --label 8 --quiet