plastid.bin.counts_in_region module

Count the number of read alignments covering regions of interest in the genome, and calculate read densities (in reads per nucleotide and in RPKM) over these regions.

Results are output as a table with the following columns:

Name	Definition
region_name	Name or ID of region of interest
region	Genomic coordinates of region, formatted as described in plastid.genomics.roitools.SegmentChain.from_str()
counts	Number of reads mapping to region
counts_per_nucleotide	Read density, measured in number of reads mapping to region, divided by length of region
rpkm	Read density, measured in RPKM
length	Region length, in nucleotides

If a mask annotation file is supplied, masked portions of regions will be excluded when tabulating counts, measuring region length, and calculating counts_per_nucleotide and rpkm.

See also

cs script

Count the number of read alignments and calculate read densities (in RPKM) specifically for genes and sub-regions (5’ UTR, CDS, 3’ UTR), excluding positions covered by multiple genes

plastid.bin.counts_in_region.main(argv=['-T', '-E', '-b', 'html', '-d', '_build/doctrees', '-D', 'language=en', '.', '_build/html'])

Command-line program

Parameters

argvlist, optional

A list of command-line arguments, which will be processed as if the script were called from the command line if main() is called directly.

Default: sys.argv[1:]. The command-line arguments, if the script is invoked from the command line