operondemmo: an independent demo of KNOWN operon predict method
Dependencies
Install
PyPI
$ pip3 install operondemmo --useror download operondemmo and install:
$ pip3 install operondemmo-*.tar.gz --userTo upgrade to latest version:
$ pip3 install --upgrade operondemmo --userGitHub
$ wget https://github.com/GodInLove/operondemmo/archive/master.zip
$ unzip operondemmo-master.zip
$ cd operondemmo-master
$ python3 setup.py installor download and install:
$ pip install operondemmo-*.tar.gzUsage
Quick start
$ operondemmo -i input_dir -f fna_file_path -g gff_file_pathOutputs: test/OUT/operon.txt
Or:
$ operondemmo -i input_dir -f fna_file_path -g gff_file_path -o out_dir -t thresholdBasic 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:
-
- 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.
- Bray N L, Pimentel H, Melsted P, et al. Near-optimal probabilistic RNA-seq quantification[J]. Nature biotechnology, 2016, 34(5): 525.
