6.3.3.7. wig2bed¶
The wig2bed script converts both variable - and fixed -step, 1-based, closed [start, end] UCSC Wiggle format (WIG) to sorted, 0-based, half-open [start-1, end) extended BED data.
For convenience, we also offer wig2starch, which performs the extra step of creating a Starch-formatted archive.
The utility also supports multiple embedded WIG sections in a single file, which are output to a single file or split into multiple BED files with the --multisplit option.
6.3.3.7.1. Source¶
The wig2bed and wig2starch conversion scripts are part of the binary and source downloads of BEDOPS. See the Installation documentation for more details.
6.3.3.7.2. Usage¶
The wig2bed script parses WIG from standard input and prints sorted BED to standard output. The wig2starch script uses an extra step to parse WIG to a compressed BEDOPS Starch-formatted archive, which is also directed to standard output.
Tip
By default, all conversion scripts now output sorted BED data ready for use with BEDOPS utilities. If you do not want to sort converted output, use the --do-not-sort option. Run the script with the --help option for more details.
Tip
If you are sorting data larger than system memory, use the --max-mem option to limit sort memory usage to a reasonable fraction of available memory, e.g., --max-mem 2G or similar. See --help for more details.
6.3.3.7.3. Example¶
To demonstrate these scripts, we use a sample WIG input called foo.wig (see the Downloads section to grab this file). We can convert WIG to sorted BED data in the following manner:
$ wig2bed < foo.wig
chr1 147971109 147971159 id-1 -0.590000
chr1 147971147 147971197 id-2 0.120000
chr1 147971185 147971235 id-3 0.110000
chr1 147971223 147971273 id-4 -0.760000
...
Note
Note the conversion from 1- to 0-based coordinate indexing, in the transition from WIG to BED. While BEDOPS supports 0- and 1-based coordinate indexing, the coordinate change made here is believed to be convenient for most end users.
Note
Multiple WIG sections in the input file are merged together by the default wig2bed behavior. When using the --multisplit option, each WIG section instead receives its own output file.
