editing of strand, score, etc

[daler]

editing of strand, score, etc

[vsmalladi]

Instead of an add_strand function, would a generic extend_bed function that allows you to extend the bed object you currently and populate these fields with . and then allow you to use the each function to add corresponding values?

[daler]

If I understand correctly, you mean something like:

def extend_fields(feature, n):
    fields = feature.fields[:]
    while len(fields) < n:
        fields.append('.')
    return pybedtools.create_interval_from_list(fields)

Then you can write a user-defined function that assumes the fields have been padded:

def add_strand(feature, strand):
    feature[5] = strand
    return feature

So you would use them like this:

import pybedtools
x = pybedtools.example_bedtool('venn.b.bed')
y = x.each(extend_fields, 6).each(add_strand, '+').saveas()

I think that works pretty well. It leaves the manipulation of the number of fields (BED, GFF, VCF) up to the user, which I would prefer since it maintains flexibility. I'll add this to pybedtools.featurefuncs in Cython so it's hopefully faster.

[vsmalladi]

That exactly what I was getting at. Sorry for not being very clear. I would also change the name from add_feature to update feature at that point, since the field would already exist.

[daler]

OK, I added extend_fields in 5cc273b -- thanks for the suggestion.

Rather than make separate functions for every possible operation, I'd prefer to leave it up to the user to create the functions they want . . . so in this case update_strand would be up to you to write/name.

[vsmalladi]

Sounds great. Ya makes more sense for a user to make and name their own functions. Thanks for adding the functionality.