git clone --recursive https://github.com/carringtonlab/p-sams.git

cp ./include/example.psams.conf ./psams.conf

# Log into MySQL
# Create an empty database
CREATE DATABASE psams_[species];

# Grant select permissions to the P-SAMS user. Add additional security as necessary.
GRANT SELECT ON psams_[species].* TO 'psams_user'@'%';

# Use the mysql command-line tool to inialize the empty database with the P-SAMS schema
mysql -u admin_user -p psams_[species] < ./p-sams/include/structure.mysql

# Switch to the new database
USE psams_[species];

# Load the kmer file
LOAD DATA INFILE 'kmers.tab' INTO TABLE kmers FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';

# Load the annotation file
LOAD DATA INFILE '[species].annotation.txt' INTO TABLE annotation FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';

usage: psams.pl [-f FASTA] [-a ACCESSIONS -s SPECIES] [-t FOLDBACK] [-c CONSTRUCT] [-o] [-h]

Plant Small RNA Maker Suite (P-SAMS).
  Artificial microRNA and synthetic trans-acting siRNA designer tool.

arguments:
  -t FOLDBACK           Foldback type [eudicot, monocot]. Default = eudicot.
  -f FASTA              FASTA-formatted sequence. Not used if -a is set.
  -a ACCESSION          Gene accession(s). Comma-separated list. Not used if -f is set.
  -s SPECIES            Species. Required if -a is set.
  -c CONSTRUCT          Construct type (amiRNA, syntasiRNA). Default = amiRNA.
  -o                    Predict off-target transcripts? Filters guide sequences to minimize/eliminate off-targets.
  -h                    Show this help message and exit.

usage: amiRNA_oligoDesigner.pl -s SEQUENCE -n NAME -t TYPE [-h]

Plant Small RNA Maker Suite (P-SAMS).
  Artificial microRNA oligo designer tool.

arguments:
  -s SEQUENCE           Artificial microRNA sequence. Must be 21-nucleotides long.
  -n NAME               Artificial microRNA name.
  -t TYPE               Foldback type. Options = eudicot or monocot.
  -h                    Show this help message and exit.

usage: syntasiRNA_oligoDesigner.pl -s SEQUENCES -n NAMES [-h]

Plant Small RNA Maker Suite (P-SAMS).
  Synthetic trans-acting siRNA oligo designer tool.

arguments:
  -s SEQUENCES           Syn-tasiRNA sequences. A comma-separated list of one or more 21-nucleotides long sequences.
  -n NAMES               A comma-separated list of names for the syn-tasiRNA sequences. Length must match the sequences list.
  -h                     Show this help message and exit.

usage: phytozome2psams.pl -f FASTA -a ANNOTATION -s SPECIES -v VERSION [-h]

Plant Small RNA Maker Suite (P-SAMS).
  Parse Phytozome transcript FASTA and annotation files.

arguments:
  -f FASTA              FASTA-formatted transcript file (*.transcript.fa).
  -a ANNOTATION         Gene annotation file (*.annotation_info.txt).
  -s SPECIES            Species name. No spaces, will be used in output file names.
  -v VERSION            Species annotation/assembly version. Will be used in output file names.
  -h                    Show this help message and exit.

usage: add_species.pl -f FASTA -s SPECIES -k KSIZE [-h]

Plant Small RNA Maker Suite (P-SAMS).
  Adds a new species to the kmer database.

arguments:
  -f FASTA              FASTA-formatted transcript sequences.
  -s SPECIES            Species code.
  -k KSIZE              Kmer length.
  -h                    Show this help message and exit.