Two R scripts which take the output of fasta_windows (version 2) and aggregates them.
fw_group groups the output statistics file (containing GC content etc) into larger windows, and operating an aggregation function in the process. fw_canon canonicalises a kmer frequency array file from fasta_windows output.
Run Rscript fw_group.R -h to display the help.
usage: fw_group.R [-h] [-t TSV] [-w number] [-g number] [-r number]
[-f string] [-c]
optional arguments:
-h, --help show this help message and exit
-t TSV, --tsv TSV input TSV file from fasta_windows output.
-w number, --window number
Size of window used in fasta_windows [fixed at 1000]
-g number, --group number
Size of window to group into [default 10000]
-r number, --round number
Round numbers to this many decimal places. Must be < 3
[default 3]
-f string, --function string
Function to apply to groups [default mean: other
options are Mode, median, var, sd]
-c, --chromosomal Aggregate statistics at the chromosomal level?
Currently only fasta windows output with 1kb windows is supported.
Rscript fw_group.R -t <TSV>
Running on fasta windows output (1kb windows) without any flags will average statistics across 10kb windows.
Rscript fw_group.R -t <TSV> -g 100000
Will average statistics across 100kb windows. 1Mb (1000000) averaging also supported.
Rscript fw_group.R -t <TSV> -f var
Calculates variance of the statistics, instead of default mean.
Rscript fw_group.R -t <TSV> -c
Adding -c or --chromosomal averages across the contigs/scaffolds/chromsomes.
Note that these statistics will be different from running fasta windows at a larger window size.
Output is printed to stdout.
usage: fw_canon.R [-h] [-t TSV]
optional arguments:
-h, --help show this help message and exit
-t TSV, --tsv TSV input TSV file from fasta_windows output.
Only requires the dinuc/trinuc/tetranucleotide frequency array file. Prints to stdout.