This R script takes the output from the
blast.pl script, a hash file containing query names and their respective chromosome numbers (
queryIndex),
a hash file containing hit names and their respective chromosome
numbers (
hitIndex), and a hash file containing the coordinates of the intron/exon
boundaries (
IntEx). The script outputs one
PDF file per target
sequence. Each
PDF file contains a diagram which shows all hits
from the list of query sequences that have matches against the target
with a significance level at or below the e-value passed to
blast.pl.
*These files must all be in the same directory as the R script.
Before this script can be run, you must ensure that there is a sub-directory named "pdfs". The script creates
PDF files
and places them there. If no such directory is created the
following error (or something similar) will be generated:
Error in pdf(paste(outDir, targetName, ".pdf", sep = ""), width = pageWidth, :
unable to start device pdf