Viral Family Frequency

To create Figure with viral family annotations for several samples:

Rscript FamilyTypes.R input_file.tsv

that script creates Viral_types.pdf Figure.

Input file(input_file.tsv) format has header and data:

files   sample_names
file_name1  label1
file_name2  label2
file_name3  label3

where each file_name* is tab-separated file with at least 2 columns: contig name and family(see file DNAmod_sample_contig_annotation.tsv as an example), label is used on Figure for that file. The file_name* can be produced by ContigAnnotation script.

#Genome Coverage and Depth

Coverage, Depth and Number of Reads mapped to Contigs

Number of reads mapped produced by samtools:

samtools idxstats file.bam > result_idxstats.dat

BAM file should be sorted and indexed.

Family Read Count

# only need to read once for specific set of contigs
contig_annotation <- read_contig_annotation(contig_annotation_file) 

# for each sample mapped to contigs:
# read file
contig_read_count <- read_contig_to_read_count(idxstats_file)
# merge 
contig_read_count_family <- add_family_annotation(contig_read_count, contig_annotation)
# summarize count for each family
family_read_count <- get_family_to_read_count(contig_read_count_family)

Or we can use a wrapper function for mulsiple samples:

contig_annotation <- read_contig_annotation("sample_contig_annotation.txt")

samples <- data.frame(
    idxstats_file=c("sample_idxstats.txt", "sample_idxstats_2nd.txt"),
    sample_name=c("Sample1", "Sample2")
)

families <- viral_familes(samples, contig_annotation)

Testing

run the following in R console:

library(testthat)
test_dir(".")