Skip to main content

an independent demo of KNOWN operon predict method

Project description

PyPI version Docs License

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for operondemmo, version 0.0.18
Filename, size File type Python version Upload date Hashes
Filename, size operondemmo-0.0.18.tar.gz (25.3 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page