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HOW_TO_launch_example.txt
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##################################################################################################################################################################
##################################################################################################################################################################
# command line to run the example analysis:
python3 EasyPrimer.py -in Example.fas
##################################################################################################################################################################
##################################################################################################################################################################
# If you are using EasyPrimer for an article or scientfic publication Please cite M. Perini et al. 2020 (https://doi.org/10.1038/s41598-020-57742-z)
# TEST FILE ==> https://skynet.unimi.it/wp-content/uploads/easy_primer/pgi.fas
# OUTPUT EXAMPLE ==> https://skynet.unimi.it/wp-content/uploads/easy_primer/pgi_HRM_analysis.pdf
# Online version of the tool: https://skynet.unimi.it/index.php/tools/easyprimer/
Developed by Matteo Perini, 2018
python EasyPrimer.py -h
usage: EasyPrimer.py [-h] [-out OUT_FOLDER] [-tmp TMP_FOLDER] [-aln ALN]
[-consthr CONSENSUS_LIMIT] [-minpri MINPRI]
[-maxpri MAXPRI] [-minamp MINAMP] [-maxamp MAXAMP]
[-prithr PRIM_THR] [-ampthr AMP_THR] [-npri N_ADJ]
[-wnpri W_ADJ] [-prefix JOBNAME] [-snp {HRM,ALL}] -in
INPUTFILE
**********
EasyPrimer was developed to assist pan-PCR and
High Resolution Melting (HRM) primer design
**********
TEST FILE ==> https://skynet.unimi.it/wp-content/uploads/easy_primer/pgi.fas
OUTPUT EXAMPLE ==> https://skynet.unimi.it/wp-content/uploads/easy_primer/pgi_HRM_analysis.pdf
optional arguments:
-h, --help show this help message and exit
-out OUT_FOLDER Output Folder. Default = 'Out'
-tmp TMP_FOLDER folder with tmp and log files, created automatically if it doesn't exist. Default = 'tmp'
-aln ALN write 'n' to skip sequence alignment. In this case the sequences must be already aligned and the file in the Current Working Directory
-consthr CONSENSUS_LIMIT
Consensus sequence limit, positive real number between 0 and 1. Default = 0.05
-minpri MINPRI Minimum primer lenght. Default = 15
-maxpri MAXPRI Maxium primer lenght. Default = 25
-minamp MINAMP Minimum amplicon lenght. Default = 40
-maxamp MAXAMP Maximum amplicon lenght. Default = 90
-prithr PRIM_THR Variability threshold for the selection of the primers, positive real number between 0 and 1. Default = 0.2
-ampthr AMP_THR Variability threshold for the selection of the amplicon, positive real number between 0 and 1. Default = 0.95
-npri N_ADJ Number of primer residues next to the aplicon considered fundamental for primer anneling. default = 5
-wnpri W_ADJ Weight for the adjustment in the '-npri' residues, positive real number between 0 and 1. default = 0.7
-prefix JOBNAME Job name to be added as a prefix in final PDF and in tmp files as well
-snp {HRM,ALL} Either 'HRM' or 'ALL', dafault is 'HRM'
required arguments:
-in INPUTFILE REQUIRED ARGUMENT: fasta file of the gene to be analyzed
If you are using EasyPrimer for an article or scientfic publication
Please cite M. Perini et al. 2020 (https://doi.org/10.1038/s41598-020-57742-z)
Online version of the tool: https://skynet.unimi.it/index.php/tools/easyprimer/