This is a series of code, input data, and output files that accompany the manuscript "Viral Genomes by the Numbers: A Comprehensive Quantitative Exploration of Thousands of Viruses" by Gita Mahmoudabadi and Rob Phillips. If using these scripts or data, please cite our manuscript.
All code is written in Python (Jupyter notebooks). Below you can find a description of each notebook. These notebooks all share in common the very first block of code (and its slight variations), wherein rawdata is read from all_rpt, all_ptt, and all_faa directories, and relevant genomic parameters for each virus, such as genome length, number of protein-coding genes, among other parameters, are stored in lengthData. The list of Jupyter notebooks and their function is shown below:
- virusHostHistogramsFV.ipynb (used to create Figure 2)
- viromePieChartsFV.ipynb (used to create Figure 2)
- geneLengthsFV.ipynb (used to create Figure 4)
- percentNoncodingFV.ipynb (used to create Figure 5)
- genomeLengthsFV.ipynb (used to create Figure 3 and SI Figure 2)
- geneOrderAndGeneAbundanceFV.ipynb (used to create Figures 6 and 7)
- viralAttachmentSites.ipynb (used to create SI Figure 3)
- viralBacterialBlast.ipynb (used to create SI Figures 4 through 9)
Most scripts will require the following dependencies (Note, using Anaconda, the installation can be as easy as running a command such as: "conda install seaborn"):
- Python 3.4+
- ete-toolkit (3.0) (pip install https://github.com/jhcepas/ete/archive/3.0.zip)
- scipy
- pandas
- Bio
- os
- numpy
- matplotlib
- seaborn
- io
- re
- random
- functools
The following should be in the working directory (i.e. the directory where the scripts are):
- all_rpt (provided as zipped directory, make sure to unzip the directory)
- all_ptt (provided as zipped directory, make sure to unzip the directory)
- all_faa (provided as zipped directory, make sure to unzip the directory)
- folderToHostTaxid.txt
- blastBacterialFinalv2
- phageProteins
- bactBlastOutputAnalyzedTopHitsV2.txt
- terminaseLmatrix.txt
- terminaseSmatrix.txt
- attLeftNumIdenSeqsMatrix.csv
- attLeftSeqPercentIdentityMatrix.csv
- accPhages.txt
- attSitePosDetail1
Output files that are included:
- textFile-1.txt
- textFile-2.txt
- textFile-3.txt
- textFile-4.txt