AutoFuz is a webscraping tool to automate the retrieval of liquid-liquid phase separation. For more info, please visit the Official FuzDrop Website.
The program takes a list of protein sequences in Fasta format (header included) and submits them to the FuzDrop website. This is a simple tool, and therefore a lot of responsibility falls on the user to insure the program works correctly. For example, the file provided to the program for input values must be valid Fasta entries recognized by FuzDrop. The program currently does not have any error recovery, so if the entry is invalid the program will crash. Secondly, the values in the input file should be separated by a newline character (enter, return, etc.). There can be other forms of whitespace in the entries because FuzDrop recognizes the values regardless.
Once the input file has been prepared, make sure python is installed on the system. If it is not, you can download it here. Then simply execute the python file (.py) via the command line or by opening the file. The command line is recommended to view error reports and live updates. A small GUI will show up prompting for some information before running the program. Timeout specifies the maximum amount of time the program will wait for each page to load. It defaults to 10 which seems to work good enough for most purposes, but if the internet speed is slow may need to be adjusted. Choose the input file that was prepared previously. Create a new file to output the data by clicking the button and typing the name of the file as well as the type (Ex. output.txt). Windows may be hidden to avoid cluttering the computer. Finally, click start and wait for the program to finish.
The output will be in the format Uniprot#: Probability where probability is a maximum of 3 decimals of precision,
separated by newline characters. Since there is a lot of variance involved with webscraping, the program may not always work on the first try. To combat this
the best I can, I have configured the output to write to the file as the program obtains the values, meaning if
the program crashes, previous values will still be stored. There also may be delays, but that does not mean the program has stopped. Please wait until there is an error message in the output to terminate the program preemptively.
It is also recommended to verify the number of entries in the output file prior to using the data, as it is possible an entry was omitted without error if running the program without the command line.
Big thanks to Shivam Shukla for helping me understand the biology aspect of this :)
Mozilla Public License 2.0
See LICENSE file