operondemmo 0.0.11

an independent demo of KNOWN operon predict method

• Dependencies

• Install

  • PyPI

  • GitHub

• Usage

  • Quick start

  • Basic Parameters

  • Advanced Parameters

Dependencies

• Python3.6

• Numpy

• Pandas

• Linux(Fedora)

• Kallisto

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 and install:

$ pip install operondemmo-*.tar.gz

Usage

Quick start

$ mkdir test
$ wget http://lyd.ourblogs.me/operondemmo/test/count.tar.gz
$ wget http://lyd.ourblogs.me/operondemmo/test/gff/eco.gff
$ cd tar -zxf count.tar.gz
$ rm -f count.tar.gz
$ operondemmo -i count -g eco.gff

Outputs: test/OUT/operon.txt

Basic Parameters

-h

PRINT_HELP: show this help message and exit

-i

INPUT_DIR: A directory to store a group of files.

-o

OUTPUT_DIR: A directory include output data(operon file).

-g

GFF_FILE: The gff file of the prokaryote

-t

THRESHOLD the threshold in (-1,1)

INPUT_DIR:

default: [samtools depth] result files

example_count/
  SRR6322033_count.txt
  SRR6322035_count.txt
  SRR6322037_count.txt
  ...

or when --kallisto

example_input/
   eco.fna
   SRR6322033_1.fastq.gz
   SRR6322033_2.fastq.gz
   SRR6322035_1.fastq.gz
   SRR6322035_2.fastq.gz
   SRR6322037_1.fastq.gz
   SRR6322037_2.fastq.gz
   ...

Advanced Parameters

--person

Build co-expression matrix with person correlation

--spearman

Build co-expression matrix with spearman correlation

--kallisto

Build expression matrix with kallisto result

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.