Util PERL module of general functions and objects applied in bioinformatics software development.

• Author: Wenlong Jia
• Email: wenlongkxm@gmail.com

0.16

2022-04-03

BioFuse is written in PERL. All of its functions are packaged into a standalone PERL module. Besides, it also requires other additional modules.

To install BioFuse, you need to download BioFuse and add the current directory to the PERL5LIB path.

git clone https://github.com/Nobel-Justin/BioFuse.git
PERL5LIB=$PERL5LIB:$PWD; export PERL5LIB

List of additional PERL modules required:

• Carp
• JSON
• List::Util
• Math::Trig
• POSIX
• LWP::UserAgent

If you encounter problems, please open an issue at the project on Github.

Besides of functions as perl modules, BioFuse also provides several commands.

• get_tpsl

  get_tpsl generates the transcripts PSL file from GTF file.

• get_gpsl

  get_gpsl generates the gene PSL file from GTF file.

• psl_seq

  psl_seq generates the FASTA file of transcripts (tpsl) or genes (gpsl).

• pslToBed

  pslToBed generates BED of genetic regions from PSL file.

• mut_fa

  mut_fa generates FASTA file based on given mutations.

• prot_dom

  prot_dom fetches domain information from online database.