add a function to create splice sites similar to create_introns

[Juke34]

I needed a function to create splice sites features easily. I propose a create_splice_sites function to do it similar to the create_introns function.
Maybe not optimal because it loops twice (one for the left splice site and once for the right splice site) over the interfeatures function but I didn't succeed to make it work differently.
The loop occurs before

for child in child_gen():
                exons = self.children(
                    child, level=1, featuretype=exon_featuretype, order_by="start"
                )

[daler]

Thanks. Can you add tests (at the bottom of gffutils/test/test.py) for this? You can run the tests locally with pytest. Still working out how to approve GitHub Actions to run on PRs from a fork, so this is not happening automatically.

[Juke34]

Hi, I didn't succeed to write a proper test. I'm not proficient enough in pytest.
I wanted to use test/data/gff_example1.gff3 as input.
The expected output is:

chr1	ensGene	gene	4763287	4775820	.	-	.	Name=ENSMUSG00000033845;ID=ENSMUSG00000033845;Alias=ENSMUSG00000033845;gid=ENSMUSG00000033845
chr1	ensGene	mRNA	4764517	4775779	.	-	.	Name=ENSMUST00000045689;Parent=ENSMUSG00000033845;ID=ENSMUST00000045689;Alias=ENSMUSG00000033845;gid=ENSMUSG00000033845
chr1	ensGene	CDS	4775654	4775758	.	-	0	Name=ENSMUST00000045689.cds0;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.cds0;gid=ENSMUSG00000033845
chr1	ensGene	CDS	4772761	4772814	.	-	0	Name=ENSMUST00000045689.cds1;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.cds1;gid=ENSMUSG00000033845
chr1	ensGene	exon	4775654	4775779	.	-	.	Name=ENSMUST00000045689.exon0;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.exon0;gid=ENSMUSG00000033845
chr1	ensGene	exon	4772649	4772814	.	-	.	Name=ENSMUST00000045689.exon1;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.exon1;gid=ENSMUSG00000033845
chr1	ensGene	exon	4767606	4767729	.	-	.	Name=ENSMUST00000045689.exon2;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.exon2;gid=ENSMUSG00000033845
chr1	ensGene	exon	4764517	4764597	.	-	.	Name=ENSMUST00000045689.exon3;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.exon3;gid=ENSMUSG00000033845
chr1	ensGene	five_prime_UTR	4775759	4775779	.	-	.	Name=ENSMUST00000045689.utr0;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.utr0;gid=ENSMUSG00000033845
chr1	ensGene	three_prime_UTR	4772649	4772760	.	-	.	Name=ENSMUST00000045689.utr1;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.utr1;gid=ENSMUSG00000033845
chr1	ensGene	three_prime_UTR	4767606	4767729	.	-	.	Name=ENSMUST00000045689.utr2;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.utr2;gid=ENSMUSG00000033845
chr1	ensGene	three_prime_UTR	4764517	4764597	.	-	.	Name=ENSMUST00000045689.utr3;Parent=ENSMUST00000045689;ID=ENSMUST00000045689.utr3;gid=ENSMUSG00000033845
chr1	gffutils_derived	three_prime_cis_splice_site	4764598	4764599	.	-	.	Name=ENSMUST00000045689.exon2,ENSMUST00000045689.exon3;Parent=ENSMUST00000045689;ID=three_prime_cis_splice_site_ENSMUST00000045689.exon2-ENSMUST00000045689.exon3;gid=ENSMUSG00000033845
chr1	gffutils_derived	three_prime_cis_splice_site	4767730	4767731	.	-	.	Name=ENSMUST00000045689.exon1,ENSMUST00000045689.exon2;Parent=ENSMUST00000045689;ID=three_prime_cis_splice_site_ENSMUST00000045689.exon1-ENSMUST00000045689.exon2;gid=ENSMUSG00000033845
chr1	gffutils_derived	three_prime_cis_splice_site	4772815	4772816	.	-	.	Name=ENSMUST00000045689.exon0,ENSMUST00000045689.exon1;Parent=ENSMUST00000045689;ID=three_prime_cis_splice_site_ENSMUST00000045689.exon0-ENSMUST00000045689.exon1;gid=ENSMUSG00000033845
chr1	gffutils_derived	five_prime_cis_splice_site	4767604	4767605	.	-	.	Name=ENSMUST00000045689.exon2,ENSMUST00000045689.exon3;Parent=ENSMUST00000045689;ID=five_prime_cis_splice_site_ENSMUST00000045689.exon2-ENSMUST00000045689.exon3;gid=ENSMUSG00000033845
chr1	gffutils_derived	five_prime_cis_splice_site	4772647	4772648	.	-	.	Name=ENSMUST00000045689.exon1,ENSMUST00000045689.exon2;Parent=ENSMUST00000045689;ID=five_prime_cis_splice_site_ENSMUST00000045689.exon1-ENSMUST00000045689.exon2;gid=ENSMUSG00000033845
chr1	gffutils_derived	five_prime_cis_splice_site	4775652	4775653	.	-	.	Name=ENSMUST00000045689.exon0,ENSMUST00000045689.exon1;Parent=ENSMUST00000045689;ID=five_prime_cis_splice_site_ENSMUST00000045689.exon0-ENSMUST00000045689.exon1;gid=ENSMUSG00000033845

The interesting features are the 6 last lines.

I didn't find any test for create_introns to get inspired from...
Could you help?

[daler]

I bet you weren't doing anything wrong -- I just found out that gffutils/test/test.py has not been running since porting tests from nosetests to pytest! Renaming the file did the trick. I added the new test in there, and I'll merge into 0.12rc branch.

[daler]

No need for this now, but I wonder if iterating over the exons in pairs (e.g. with itertools.pairwise or similar) would make this and create_introns more efficient.