plotMyGBK is a very simple to use pipe that use a genbank file and give you a nice circular graph (using omiccircos to make the graph)
- Python >= 2.7 with the module Biopython
- R (tested in 3.2.3), and the following libraries:
##Installation
- If you want to classify your genes by functions, download the zip from here, and unzip. This package have all neccesary files to classify your genes using the COG Assignments.
- Download the script from this repository and put them together with data folder that you unzipped previously.
plotMyGBK have minimal use:
python plotMyGBK.py -f mygenbank.gbk
and a complete use:
python plotMyGBK.py -f mygenbank.gbk -C Y -F Y -w 3000 -s 1500 -t 16
- -f is the genbank file
- -C Cog Assign, this will call to rpsblast (provided in data folder, v=2.2.31+), and classify the genes by Cog function. default=N
- -F Filter Contigs, show only contigs that have genes. default=Y
- -w Windows size, to computing GC content and GC skew set the windows size, default:3000
- -s Step size, size in bp to move windows (-w), default:1500
- -t Threads, threads for rpsblast
##Trick
plotMyGBK first search for rpsblast out (format 6), if this file exists, you can save a lot of time!, put this file together with the scripts and change the name to: rpsblast.GBKNAME.faa.out where GBKNAME is the name of your gbk file included the extension .gbk (e.g. mygbk.gbk ==> rpsblastout.mygbk.gbk.faa.out)
##Output
Since your gbk, plotMyGBK will generate a folder called results_GBKNAME.faa where GBKNAME is the genbank file, this folder contain several files like faa, fna, parsed rpsblast results, other files necessaries to plot and last the plot in pdf format.
##Notes
- When you execute plotMyGBK.py make sure data folder and plotstep.R are in that directory.
- The rpsblast in the data folder was compiled in Mac OSX, if you use other OS, you have to put the corresponding binary of rpsblast in this data folder
##References
- Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Lie- bert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH: CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res 2003, 31:383-387
- Ying Hu Chunhua Yan yanch@mail.nih.gov (2015). OmicCircos: High-quality circular visualization of omics data. R package version 1.8.1.