A python tool for identify rRNA gene in plant genome.
Project description
rRNAFinder
A python tool for identify rRNA gene in plant genome.
Installation
This package depended on ncbi blast, you should install it first.
Install rRNAFinder with pip:
pip install rRNAFinder
Usage
usage: rRNAFinder [-h] [-s QUERY_RRNA_SEQ] [-b QUERY_RRNA_BED] [-l LOG_FILE] [-o OUTPUT_DIR] fasta_file
Find rRNA unit and all rRNA in genome
positional arguments:
fasta_file a fasta file
optional arguments:
-h, --help show this help message and exit
-s QUERY_RRNA_SEQ, --query_rRNA_seq QUERY_RRNA_SEQ
a known rRNA unit seq from close species
-b QUERY_RRNA_BED, --query_rRNA_bed QUERY_RRNA_BED
bed file for close rRNA unit seq
-l LOG_FILE, --log_file LOG_FILE
path for log file (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
output prefix (default: rRNA_finder)
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