8000 `intersect` with multiple `-b` arguments · Issue #156 · daler/pybedtools · GitHub
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intersect with multiple -b arguments #156

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daler opened this issue Jan 24, 2016 · 0 comments
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intersect with multiple -b arguments #156

daler opened this issue Jan 24, 2016 · 0 comments

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@daler
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daler commented Jan 24, 2016

In recent BEDTools versions, intersect can accept a list of filenames as the -b argument. pybedtools has long supported flexible input types for b, for example:

  • filename
  • pybedtools.BedTool object
  • list of (chrom, start, stop) tuples
  • list of pybedtools.Interval objects
  • list of strings (passed directly to stdin)

It's this last one that causes a problem. There's currently no heuristic to determine whether a list of strings should be considered filenames or intervals.

I think this can be solved by checking to see if the first item in the list can be converted to an Interval object. Consuming an input iterator would be avoided if this check is only done if the input is a list. That means filenames can't be provided as iterators, but hopefully that shouldn't be a problem.
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