Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
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@ryan-c-thompson-5618
Last seen 12 months ago
Scripps Research, La Jolla, CA

I have a BED file from an external data source that is tab-separated with spaces in the name field for some rows. These fields are not quoted. Looking at the code for rtracklayer::import.bed, it seems to use read.table with the default separator argument and no option to change it, which means all whitespace is treated as field separators. This causes the import to fail. Would it be possible to add an option to specify the separator when importing BED files?

rtracklayer bed software error • 659 views
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@michael-lawrence-3846
Last seen 6 weeks ago
United States

I just pushed a change to devel that expects all BED files to be tab-separated. That's what the spec says, and it's what bedtools requires, so hopefully it does not cause too much havoc.

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Sounds good to me.

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