Search

bigsi search --help

usage: search [-h] [-d DB] [-s SEQ] [-se SEQFILE] [-t THRESHOLD]
                   [-o {json,tsv,fasta}] [-p] [-pi] [-c CACHESIZE] [-sc]

optional arguments:
  -h, --help            show this help message and exit
  -d DB, --db DB        Basic text / string value
  -s SEQ, --seq SEQ     Basic text / string value
  -se SEQFILE, --seqfile SEQFILE
                        Basic text / string value
  -t THRESHOLD, --threshold THRESHOLD
                        A float number
  -o {json,tsv,fasta}, --output_format {json,tsv,fasta}
                        Accepts one of the following values: (json|tsv|fasta)
  -p, --pipe_out        Accepts a true or false value
  -pi, --pipe_in        Accepts a true or false value
  -c CACHESIZE, --cachesize CACHESIZE
                        A Whole number
  -sc, --score          Accepts a true or false value

E.g. Searching a fasta of sequence

Below is the command to search for all staph amr genes from Mykrobe predictor.

bigsi search -p -o tsv --seqfile ~/git/Mykrobe-predictor/mykrobe/data/panels/staph-amr-bradley_2015-feb-17-2017.fasta --db /ssd0/sra/