with_column name change?

[daler]

with_column name change?

[brentp]

maybe it should be called each and the function just gets a feature so like:

def modify_feature(feat):
    feat.name = feat.name + "-" + str(feat.start)
    if feat.chrom.startswith("chr"): feat.chrom = feat.chrom[3:]
    return feat

bed.each(modify_feature)

then we'd just have to implement feat.add_column() in case they want to add an additional column.

[daler]

Yeah, this is way better than the awkward column manipulation. Do we have to worry about making copies to pass to modify_feature, or just assume that the iterator is making 'throwaway' Intervals that, if needed again, will be read straight from the file anyway?

[brentp]

oh, right. hadn't thought about that. better make a copy (and implement feat.copy() :-) )
if you have any trouble, i can hack on this later as it'll be in the cython i'm familiar with that part of the code.
but you can use create_interval_from_list or create_interval from within cython.

[daler]

i should hack on it myself to get familiar with the cython part, but won't get around to it until later. either way, i'm sure i'll learn a lot from seeing how you implement it.

[daler]

closing cause these ideas are now implemented in BedTool.each