an independent demo of KNOWN operon predict method
Project description
Dependencies
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:
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.
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