def test_gff3join():
#apidb|MAL1 ApiDB gene 56913 57116 . - . ID=apidb|PFA0035c;Name=PFA0035c;description=hypothetical+protein%2C+conserved+in+P.+falciparum;size=204;web_id=PFA0035c;locus_tag=PFA0035c;size=204;Alias=MAL1P4.06b
snps = (('chr', 'pos'),
('apidb|MAL1', 56911),
('apidb|MAL1', 56915))
features = fromgff3(plasmodb_gff3_file.name)
genes = selecteq(features, 'type', 'gene')
actual = gff3join(snps, genes, seqid='chr', start='pos', end='pos')
expect = (('chr', 'pos', 'seqid', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase', 'attributes'),
('apidb|MAL1', 56915, 'apidb|MAL1', 'ApiDB', 'gene', 56913, 57116, '.', '-', '.', gff3_parse_attributes("ID=apidb|PFA0035c;Name=PFA0035c;description=hypothetical+protein%2C+conserved+in+P.+falciparum;size=204;web_id=PFA0035c;locus_tag=PFA0035c;size=204;Alias=MAL1P4.06b")))
ieq(expect, actual)
ieq(expect, actual)
def test_gff3lookup():
features = fromgff3(plasmodb_gff3_file.name)
genes = selecteq(features, 'type', 'gene')
lkp = gff3lookup(genes)
#apidb|MAL1 ApiDB gene 56913 57116 . - . ID=apidb|PFA0035c;Name=PFA0035c;description=hypothetical+protein%2C+conserved+in+P.+falciparum;size=204;web_id=PFA0035c;locus_tag=PFA0035c;size=204;Alias=MAL1P4.06b
actual = lkp['apidb|MAL1'][56911:56915]
eq_(1, len(actual))
eq_(56913, actual[0][3])
eq_(57116, actual[0][4])
actual = lkp['apidb|MAL1'][56915]
eq_(1, len(actual))
eq_(56913, actual[0][3])
eq_(57116, actual[0][4])
