4‐Python‐version

Requirment

You need put Pfam database into the folder where this function is located.

You can change run_default_path into your path.

Package

biopython

You can install biopython with document.

Usage

# see help
python NRPS_motif_Finder.py -h

#python Find_motif_HRL.py -i <inputfile> -o <outputfile> -p <processid> -G <1 or 0> -A <1 or 0> -T <1 or 0> -length_threshold <length_threshold 0.6> -length_threshold_TE <length_threshold_TE 0.5>

-i: input sequence in the fasta format

-o: output of result in the json format

-p:

-G:

-A:

-T:

-length_threshold: used in hmmer scan for C/A/T domain. Value is in the range of 0~1. (default:0.6) User can reduce the threshold, if miss some known domains.

-length_threshold_TE: used in hmmer scan for TE domain. Value is in the range of 0~1. (default:0.5) User can reduce the threshold, if miss some known domains.