python v2.7
R v3.5.1
Bioconductor
STRING db-bioconductor
$R
source("https://bioconductor.org/biocLite.R")
biocLite("STRINGdb")
FOR DEBIAN USING APT
sudo apt-get install python-igraph
sudo apt-get install python-matplotlib
USING PIP
pip install python-igraph
pip install matplotlib
String_data_download.r
Stringdb_parse.py
Pairwise_dis_index.py
Pairwise_discon_vdisjoint_paths.py
Mapping_on_annotation_file.py
X.sh
$ chmod +x x.sh
$ ./x.sh
ABOUT x.sh
This is a pipeline which initialize the process and input from one script is passed to other script and at the end it will return the 3 files one with all crucial nodes ,non-crucial nodes ,moderately crucial nodes mapped onto the annotation file .This will first download the string data by taking species id from user as input Then the data will be unzipped and parsed on for the scripts which evaluates the pairwise dis connectivity index and similar using disjoint path return result files in a directory named out .
- SCRIPTS CAN ALSO BE USED AS STAND ALONE FOR USAGE AND MORE INFORMATION CHECK THE THESIS.