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>
python Find_motif_HRL.py -i test.fasta -o test -p tmp -G 1 -A 1 -T 0 -length_threshold 0.6 length_threshold_TE 0.5

-i: input sequence in the fasta format

Waring: The headers of input fasta file must be different!!!

-o: output of result in the json format

-p: the temporary MSA file name

-G: 1=use new G-motif in A domain, 0=don't use

-A: 1=use new Aalpha motif in A domain, 0=don't use

-T: 1=use new Talpha motif in T domain, 0=don't use

-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.

Note: Loop length, sequence, group and specificity-conferring codes are always in the output.