fmm_crawl

Automatic search for Biosynthesis pathway information

#AUTHOR

Byunghyun Ban

• CTO of Imagination Garden Inc. (2018~)
• CFO & CEO of Cheesecake Studio Inc. (2016 ~ 2017)
• CEO & CTO of Studio Mic Inc. (2015)
• CTO of New Page Inc. (2011~2013)
• Master's Degree @ Bio and Brain Engineering Department, KAIST (Korea Advanced Institute of Science and Technology)
• [email protected]
• [email protected]

1. Environments

• Python3
• Don't support any problems from python2 environment

2. Dependencies

• Selenium and chromedriver are required.

pip install selenium on bash.

• chromedriver for Chrome version 78. is attached. Please check the version.

3. Preperation of input file

Each line should contain one KEGG ID, without any comma.

4. Usage

python main.py <out_file_name> <from_file_name> <to_file_name>

Then the headless driver accesses to FMM server, searching all possible queries.

5. About FMM

http://fmm.mbc.nctu.edu.tw/

C.H. Chou, W.C. Chang, C.M. Chiu, C.C. Huang, and H.D. Huang (2009) "FMM: a web server for metabolic pathway reconstruction and comparative analysis", Nucleic Acids Research, Vol. 37, W129-34 [PubMed]