mapmuts_aafracsplots.py

Makes plots summarizing fractions of each different mutant amino acid at each site. This script is designed to be run after you have already run mapmuts_parsecounts.py on several samples. Each run of that program generates a *_codoncounts.txt file, which is used as input for this script.

To run this script from the prompt, first create a text infile of the format described below. Then simply type mapmuts_aafracsplots.py followed by the infile name. For example, if the name is infile.txt, type:

mapmuts_aafracsplots.py infile.txt

This script will only work if pylab / matplotlib are available.

Input file format

The input file is a text file that should have the following entries. Blank lines or lines beginning with # are ignored (i.e. as comment lines).

The first line should specify the key plotfileprefix followed by the prefix given to the plot for each site. For example, to place the plots in the directory aafracsplots with the prefix WT-1_aafracs you would use:

plotfileprefix aafracsplots/WT-1_aafracs

This would then create files aafracsplots/WT-1_aafracs_M1.pdf, etc for all sites. Note that if plotfileprefix specifies a directory as part of the prefix, that directory must already exist (so in the above example, aafracsplots/ must already exist).

There should then be a list of lines specifying the locations of the *_codoncounts.txt files created by mapmuts_parsecounts.py. Each line should give the name / location of the file (no spaces allowed), followed by the name given to that sample in the plots.

Finally, there should be a line with the key printprogress and the value being either True or False. If it is True, a progress line is printed as the script runs, indicating how many plots have been made already.

Here is an example input file:

# input file to mapmuts_aafracsplots.py
plotfileprefix aafracsplots/WT-1_aafracs
DNA/WT-1_DNA_codoncounts.txt WT-1 DNA
mutDNA/WT-1_mutDNA_codoncounts.txt WT-1 mutDNA
RNA/WT-1_RNA_codoncounts.txt WT-1 RNA
virus-p1/WT-1_virus-p1_codoncounts.txt WT-1 virus-p1
virus-p2/WT-1_virus-p2_codoncounts.txt WT-1 virus-p2
mutvirus-p1/WT-1_mutvirus-p1_codoncounts.txt WT-1 mutvirus-p1
mutvirus-p2/WT-1_mutvirus-p2_codoncounts.txt WT-1 mutvirus-p2
printprogress True

Output files

This script will generate an output plot for each site in the protein. These sites will be named with the prefix given by plotfileprefix and the suffix being the wildtype identity at that site and then the site number. For example, assuming the first residue in methionine (M), the first plot for the above example input file would be aafracsplots/WT-1_aafracs_M1A.pdf.

In general, there are going to be quite a few of these plots (for example, there will be 500 for a 500-residue protein). This is why you may want to specify a new directory with plotfileprefix.

Here is an example plot: