Dependencies

- Python3.6

- Numpy

- Pandas

- Linux(Fedora)

Install

PyPI

pip3 install operondemmo --user

or download operondemmo and install:

pip3 install operondemmo-*.tar.gz --user

to upgrade to latest version

pip3 install --upgrade operondemmo --user

Github

wget https://github.com/GodInLove/operondemmo/archive/master.zip
 unzip operondemmo-master.zip
 cd operondemmo-master
 python3 setup.py install

or download operondemmo and install:

pip3 install operondemmo-*.tar.gz --user

Usage

Quick Start

operondemmo -i input_dir -f fna_file_path -g gff_file_path

Or:

operondemmo -i input_dir -f fna_file_path -g gff_file_path -o out_dir -t threshold

Outputs: OUT/operon.txt

Input Dir

example_input/
 	c1/
		SRR6322033_1.fastq.gz
		SRR6322033_2.fastq.gz
 	c2/
		SRR6322035_1.fastq.gz
		SRR6322035_2.fastq.gz
 	c3/
		SRR6322037_1.fastq.gz
		SRR6322037_2.fastq.gz
		...

Basic Parameters

option Description
-h PRINT_HELP: show this help message and exit
-i INPUT_FILES: A directory to store a group of result files through [samtools depth XXX > xxx.txt] command
-o OUTPUT_PATH: A directory include output data(operon file).
-g GFF_FILE: The gff file of the prokaryote
-t THRESHOLD: the threshold in (-1,1)

Advanced Parameters

option Description
--person Build co-expression matrix with person correlation
--spearman Build co-expression matrix with spearman correlation

Usage on Github pages

ROC

DATA:

condition1: SRR6322033; condition2: SRR6322035; condition3: SRR6322037;

condition4: SRR6322039; condition5: SRR6322041; condition6: SRR6322043;

condition7: SRR6322045;

DATA:

condition1: SRR6048166,SRR6048167; condition2: SRR6048169,SRR6048170; condition3: SRR6048172,SRR6048173;

condition4: SRR6048175,SRR6048176; condition5: SRR6048178,SRR6048179;

About

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