GFF mode versus BED mode in pybedtools

[daler]

GFF mode versus BED mode in pybedtools

[daler]

In general, I think cases like this are best handled by using a custom function supplied to .each(). But there's an existing function gff2bed() you could use for .each():

import pybedtools
from pybedtools.featurefuncs import gff2bed
b = pybedtools.example_bedtool('d.gff')
print b

chr1    fake    gene    50  300 .   +   .   ID=gene1
chr1    fake    mRNA    50  300 .   +   .   ID=mRNA1;Parent=gene1;
chr1    fake    CDS 75  150 .   +   .   ID=CDS1;Parent=mRNA1;
chr1    fake    CDS 200 275 .   +   .   ID=CDS2;Parent=mRNA1;
chr1    fake    rRNA    1200    1275    .   +   .   ID=rRNA1;

c = b.each(gff2bed).saveas('out.bed', trackline='track name=test')
print c

track name=test
chr1    49  300 gene1   .   +
chr1    49  300 mRNA1   .   +
chr1    74  150 CDS1    .   +
chr1    199 275 CDS2    .   +
chr1    1199    1275    rRNA1   .   +

Does this do what you want?

[yarden]

Yes, thanks, this is very elegant -- did not know about gff2bed.

[daler]

Good to hear. If you have any other commonly-used transformations, I can put them in featurefuncs as well.

(closing this for now, but please reopen if needed)

[yarden]

Quick followup: Is there an equivalent bed2gff somewhere that I missed? thanks

[daler]

Just added featurefuncs.bed2gff (added in 7cff02f) -- see if this does the trick.