lkuchenb / a2mgaps

Plot MSA gap statistics from an a2m file

a2mgaps

Requirements

• numpy
• biopython
• matplotlib

Usage

a2mgaps <outpath.pdf> <inpath.a2m> [<inpath.a2m> ...] [OPTIONS]

--allcols             Include all columns in the plot (also lower case
                      characters)
--printvals           Print the numeric values in TSV format to STDOUT
--cpos CPOS [CPOS ...]
                      Concatenation position(s) for concatenated MSAs.

Example with data export

Export the gap statistics

a2mgaps <outpath.pdf> <inpath.a2m> --allcols --printvals > values.tsv

Example code in R to recreate the gap plot

library(ggplot2)
ggplot(read.table("values.tsv", header = T)) + geom_bar(aes(x=position, y=count, fill=gaptype), stat = "identity")