Basic Usage

Jaime Huerta-Cepas edited this page Sep 20, 2016 · 5 revisions

Basic Usage

HMMER based searches

  • Disk based searches on the optimized bacterial database
python emapper.py -i test/polb.fa --output polb_bact -d bact
  • Disk based searches on the optimized database of viral models
python emapper.py -i test/polb.fa --output polb_viruses  -d viruses
  • Disk based searches on the mammal specific database
python emapper.py -i test/p53.fa --output p53_maNOG -d maNOG
  • Memory based searches on the mammal specific database
python emapper.py -i test/p53.fa --output p53_maNOG -d maNOG --usemem
  • Using DIAMOND as search method.

Note that no target database is required when using DIAMOND.

python emapper.py -i test/p53.fa --output p53_maNOG  -m diamond
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