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Question: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
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gravatar for Ryan C. Thompson
5 months ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson6.3k wrote:

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?

ADD COMMENTlink modified 5 months ago by Michael Lawrence9.9k • written 5 months ago by Ryan C. Thompson6.3k
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gravatar for Michael Lawrence
5 months ago by
United States
Michael Lawrence9.9k wrote:

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.

ADD COMMENTlink written 5 months ago by Michael Lawrence9.9k

Sounds good to me.

ADD REPLYlink written 5 months ago by Ryan C. Thompson6.3k
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