operondemmo 0.0.5

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

$ git clone https://github.com/GodInLove/operondemmo.git
$ cd operondemmo
$ python3 setup.py install

or download and install:

$ pip install operondemmo-*.tar.gz

Quick start

$ git clone https://github.com/GodInLove/operondemmo.git
$ cd operondemmo/test/count && tar -zxf count.tar.gz
$ rm -f count.tar.gz
$ cd ..
$ operondemmo -i count -g gff/eco.gff

Outputs: test/OUT/operon.txt

Basic Parameters

-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

--person

Build co-expression matrix with person correlation

--spearman

Build co-expression matrix with spearman correlation

cite:

1. Junier I, Unal E B, Yus E, et al. Insights into the mechanisms of basal coordination of transcription using a genome-reduced bacterium[J]. Cell systems, 2016, 2(6): 391-401.