Circulator is a multi-threaded software that scans for CDSs in circRNA suquences. Provide an input FASTA file that contains circRNA sequence records and the software will scan and output predicted protein-formatted fasta records.
usage: Circulator.py [-h] [-o Output] [-m MIN] [-t THREADS] [-l] [-r] [-v]
Input
.__ .__ __
____ |__|______ ____ __ __| | _____ _______ _____/ |_
_/ ___\| \_ __ \_/ ___\| | \ | \__ \_ __ \/ _ \ __\
\ \___| || | \/\ \___| | / |__/ __ \| | \( <_> ) |
\___ >__||__| \___ >____/|____(____ /__| \____/|__|
\/ \/ \/
Translate potential CDSs in circRNAs.
By Amin Mahpour.
positional arguments:
Input Input FASTA file.
optional arguments:
-h, --help show this help message and exit
-o Output, --out Output
Output protein FASTA file.
-m MIN, --min MIN Cutoff CDS size. default: 20.
-t THREADS, --threads THREADS
Requested processor numbers. Default(0) uses all
available cores. example: -t 4
-l, --longest Only keep longest ORFs.
-r, --rna Input fasta file is RNA sequence.
-v, --version show program's version number and exit
Examples:
Circulator.py input.fa > output.fa #Simple usage
Circulator.py -t 4 input.fa -o output.fa #Add 4 threads
Circulator.py -t 4 -l input.fa -o output.fa #Add 4 threads and keep the longest CDS.
Circulator.py -t 4 -l -m 25 input.fa > output.fa #Add 4 threads and keep the longest CDS and set a cutoff of 25 amino acids.