view cytosine_report_to_bedgraph/bismark2bedgraph.awk @ 5:ee5badb527cd draft default tip

Uploaded

#!/usr/bin/awk

#USAGE:
#awk -v context=<list_of_contexts> -v coverage=<boolean> -f <script_path>/bismark2bedgraph.awk <cytosine_report_name> >> <bedgraph_name>

BEGIN {
	FS = "\t";
}

{
	if ( $6 ~ context && ( $4 > 0 || $5 > 0 ) ) { 

		chr_name = $1;
		chr_pos = $2;
		strand = $3;
		c_meth_count = $4;
		c_unmeth_count = $5;

		if ( coverage == "true" ) {
			nb_reads = c_meth_count + c_unmeth_count
			printf("%s\t%s\t%s\t%s\n", chr_name, chr_pos, chr_pos, nb_reads)
		} else {
			if ( strand == "-" ) { 
				s = "-"; 
			} else { 
				s = "";
			}
			meth_ratio = c_meth_count / ( c_meth_count + c_unmeth_count ); 
			printf( "%s\t%s\t%s\t%s%s\n", chr_name, chr_pos, chr_pos, s, meth_ratio )	
		}
	}
}