Commit 1e737902 authored by LCSB sysadmin's avatar LCSB sysadmin

Fix

parent 408e225d
Pipeline #1116 failed with stages
in 13 minutes and 40 seconds
......@@ -131,7 +131,6 @@ annot.1 <- as.data.frame(cbind(annot.1, annot.1$end - annot.1$start + 1))
colnames(annot.1)[ncol(annot.1)] <- "gene_length"
# aggregate table and calculate total gene lengths within contig
save.image(name_plot("mg_results.Rdat"))
print("Calculating coding density of contigs")
# Create temporary table
total_gene_length <- aggregate(gene_length~contig, data=annot.1, FUN=sum)
......@@ -151,15 +150,13 @@ annot.3 <- cbind(rownames(annot.3), annot.3, rowSums(annot.3[,c(1:ncol(annot.3))
rownames(annot.3) <- NULL
colnames(annot.3)[c(1, ncol(annot.3))] <- c("contig", "all_annotations")
save.image(name_plot("mg_results.Rdat"))
if (is.null(ncol(annot.3)))
{
print("Skipping annotation count")
annot.4 <- annot.2
}else{
annot.3 <- cbind(rownames(annot.3), annot.3, rowSums(annot.3[,c(3:ncol(annot.3))]))
rownames(annot.3) <- NULL
annot.3 <- cbind(annot.3, rowSums(annot.3[,c(3:ncol(annot.3))]))
colnames(annot.3)[c(1, ncol(annot.3))] <- c("contig", "all_annotations")
annot.4 <- merge(annot.2, annot.3, by="contig")
}
......
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