git clone https://github.com/fmidori/arachnofamtox.git ArachnoFamTox

cd ArachnoFamTox

python -m venv arachnofamtox_env
source arachnofamtox_env/bin/activate

pip install -r requirements.txt

python setup.py install 

ArachnoFamTox -fasta test.pep -out out_test_dir 

  -h, --help            show this help message and exit
  -fasta <fasta file>   Specify fasta file
  -path <string>        Specify models path. Default=db
  -eHMM <evalue>        e-value for HMMSCAN. Default=1e-1
  -ePSSM <evalue>       e-value for PSSM. Default=1e-5
  -eBLASTP <evalue>     e-value for BLASTp. Default=1e-5
  -qcovsfilter <float>  Filter BLASTp output for qcovs >= <float>. Default=Off
  -pposfilter <float>   Filter BLASTp output for ppos >= <float>. Default=Off
  -pidentfilter <float> Filter BLASTp output for pident >= <float>. Default=Off
  -evaluefilter <float> Filter BLASTp output for evalue <= <evalue>. Default=1e-10
  -cpu <int>            Specify number of threads. Default=1
  -out <output folder>  Specify directory to output
  --force               Force re-use output directory. Default=Off.
  --tempfiles           Maintain temporary files. Default=Off.

• The default PSSM and HMM models directory is "db" (default). To use ArachnoFamTox databases, make sure to run commands inside directory ArachnoFamTox.

• To test with other PSSM, HMM and BLASTp models, use flag -path to specify the directory with new models. The new models must have the same names and should be specified with -model_name. For example, files for PSSM, HMM and BLASTp are named MODEL.pssm and MODEL.hmm, inside directory "new_models":

ArachnoFamTox.py -fasta test.pep -out out_test_dir -path new_models -model_name MODEL 

Inside output directory, results files are created:

• classification_results: file with proteins classified by PSSM and HMM merged results;
• toxprot_results: file with proteins identified only by BLASTp search against ToxProtDB;
• out.pssm (optional): Output from RPS-BLAST search against ArachnoFamTox PSSM database;
• out.hmmer.domtab.parsed (optional): Output from HMMScan search against ArachnoFamTox HMM database;
• merged_outputs.tsv (optional): Temporary file with merged outputs from PSSM and HMM searches;
• out.blastp.toxprot (optional): Temporary file with toxprot search result.

• HMMER 3
  Used for HMM profile prediction.
  Eddy SR, Accelerated Profile HMM Searches. PLOS Computational Biology 2011, 10.1371/journal.pcbi.1002195

• BLAST 2.11
  Used for RPS-BLAST and BLASTp prediction.
  Altschul, Stephen F., et al. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic acids research 25.17 (1997): 3389-3402.

GPL v3

Abukawa, F.M.(2022). Abordagens computacionais para identificação e classificação de toxinas em aracnídeos e predição de peptídeos bioativos antivirais. [Master Thesis, Instituto Butantan]. Repositório do Instituto Butantan. (https://repositorio.butantan.gov.br/handle/butantan/4870)

• Fernanda Midori Abukawa