Java Input Output

Input

The Graph can be created for all the Human proteins or for a custom protein list.

By default, no input is required and all Human proteins are used. If an input file is provided, it has to be a list of proteins represented by their Uniprot Accession number, one each line. Example:

P47211
O43603
O75325
P37288
Q8IWW8
Q9BZL3
P00736
P18505
P09871
P16118
P55317

The custom input file can be specified using the -i command line argument.

Output

The result graph is a ".sif" file, with the following structure:

protein1 <interaction type> protein2
protein3 <interaction type> protein1 
protein4 <interaction type> protein5 protein6 protein2
protein7
...

By default, the result ".sif" file will be in the same location as the ".jar" file by default. A different location can be selected using the -o command line argument.

Example Output:

Q01718 io P01189
P46663 io P01042 P30411
P00736 co P0C0L4 P0C0L5
P09871 co P0C0L5 P0C0L4
P02747 co P0C0L5 P0C0L4
P62158 co P06737 P11217
P02745 co P0C0L4 P0C0L5
P30411 io P46663 P01042
P02746 co P0C0L4 P0C0L5
P0C0L5 io P0C0L4
P01189 io Q01718
P0C0L4 io P0C0L5
Q9Y6Z7 co P0C0L5 P0C0L4
Q9BWP8 co P0C0L5 P0C0L4
O00602 co P0C0L5 P0C0L4
Q15485 co P0C0L5 P0C0L4
O75636 co P0C0L5 P0C0L4
P69905 io P00738 P68871