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#!/usr/bin/env RScript
#contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
#email="m_gruenstaeudl@fhsu.edu"
#version="2024.04.08.0223"
PACVr.compileCovStats <- function(gbkData,
coverageRaw,
analysisSpecs,
outputSpecs) {
outputSpecs$makeStatsFolder()
covData <- printCovStats(gbkData,
coverageRaw,
analysisSpecs,
outputSpecs)
# Count of N nucleotides for source
regionsSummary <- getAmbigCounts(gbkData,
analysisSpecs)
# Add count of mismatches between IRs
regions_name <- analysisSpecs$regions_name
if (analysisSpecs$isSyntenyLine) {
IR_mismatches <- checkIREquality(gbkData,
analysisSpecs)
regionsSummary <- dplyr::full_join(regionsSummary,
IR_mismatches,
regions_name)
}
# Summarized coverage data, grouped by `quadripRegions`;
# add previous results to this
if (!is.null(covData)) {
summary <- getCovSummaries(covData,
analysisSpecs)
summary$regions_summary <- dplyr::full_join(summary$regions_summary,
regionsSummary,
regions_name)
} else {
summary <- list(
regions_summary = regionsSummary
)
}
writeSumTables(summary,
gbkData$sampleName,
outputSpecs$statsFilePath)
logger::log_info('Coverage statistics saved to `{outputSpecs$statsFilePath}`')
}
getAmbigCounts <- function(gbkData, analysisSpecs) {
ambigCounts <- data.frame(
N_count = unname(Biostrings::alphabetFrequency(gbkData$sequences)[, "N"])
)
ambigCounts[analysisSpecs$regions_name] <- "Complete_genome"
return(ambigCounts)
}
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