operondemmo 0.0.16

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

$ operondemmo -i input_dir -f fna_file_path -g gff_file_path

Outputs: test/OUT/operon.txt

Or:

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

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).

-f

FNA_FILE: The fna file of the prokaryote genome.

-p

PROCESS_NUM Specify the number of processing threads.

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
   ...

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.

2. Bray N L, Pimentel H, Melsted P, et al. Near-optimal probabilistic RNA-seq quantification[J]. Nature biotechnology, 2016, 34(5): 525.