def test_search_fields_singlevalue(self):
reader = BigBedReader(self.bb_indexed)
found = list(reader.search("name","should_have_no_match"))
self.assertEqual([],found)
found = list(reader.search("Name","Sam-S-RE"))
expected = [
SegmentChain(GenomicSegment('2L',106902,107000,'+'),GenomicSegment('2L',107764,107838,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RE', 'CG2674-RE']'",ID='FBtr0089437',Name='Sam-S-RE',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
]
self.assertEqual(expected,found)
found = list(reader.search("gene_id","FBgn0005278"))
expected = [
SegmentChain(GenomicSegment('2L',106902,107000,'+'),GenomicSegment('2L',107764,107838,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RE', 'CG2674-RE']'",ID='FBtr0089437',Name='Sam-S-RE',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107760,107838,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,111337,'+'),Alias='na',ID='FBtr0308091',Name='Sam-S-RK',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='110900',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107760,107838,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111004,111117,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114210,'+'),Alias="'['M(2)21AB-RB', 'CG2674-RB']'",ID='FBtr0089428',Name='Sam-S-RB',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='112741',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107760,107838,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RA', 'CG2674-RA']'",ID='FBtr0089429',Name='Sam-S-RA',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107760,107956,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias='na',ID='FBtr0330656',Name='Sam-S-RL',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='112781',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107936,108226,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114210,'+'),Alias="'['M(2)21AB-RH', 'CG2674-RH']'",ID='FBtr0089432',Name='Sam-S-RH',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107936,108101,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RD', 'CG2674-RD']'",ID='FBtr0089430',Name='Sam-S-RD',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107936,108101,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111004,111117,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RC', 'CG2674-RC']'",ID='FBtr0089431',Name='Sam-S-RC',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',108088,108226,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RF', 'CG2674-RF']'",ID='FBtr0089433',Name='Sam-S-RF',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',108132,108346,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RI', 'CG2674-RI']'",ID='FBtr0089434',Name='Sam-S-RI',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',108132,108226,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111004,111117,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RJ', 'CG2674-RJ']'",ID='FBtr0089435',Name='Sam-S-RJ',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',109593,109793,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111004,111117,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114210,'+'),Alias="'['M(2)21AB-RG', 'CG2674-RG']'",ID='FBtr0089436',Name='Sam-S-RG',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='109750',type='exon') ,
]
self.assertEqual(sorted(expected),sorted(found))
def test_search_fields_multivalue(self):
reader = BigBedReader(self.bb_indexed)
found = list(reader.search("name","should_have_no_match","should_also_have_no_match"))
self.assertEqual([],found)
found = list(reader.search("Name","Sam-S-RE","Sam-S-RK"))
expected = [
SegmentChain(GenomicSegment('2L',106902,107000,'+'),GenomicSegment('2L',107764,107838,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,110877,'+'),GenomicSegment('2L',111906,112019,'+'),GenomicSegment('2L',112689,113369,'+'),GenomicSegment('2L',113433,114432,'+'),Alias="'['M(2)21AB-RE', 'CG2674-RE']'",ID='FBtr0089437',Name='Sam-S-RE',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='113542',thickstart='108685',type='exon'),
SegmentChain(GenomicSegment('2L',107760,107838,'+'),GenomicSegment('2L',108587,108809,'+'),GenomicSegment('2L',110405,110483,'+'),GenomicSegment('2L',110754,111337,'+'),Alias='na',ID='FBtr0308091',Name='Sam-S-RK',color='#000000',gene_id='FBgn0005278',score='0.0',thickend='110900',thickstart='108685',type='exon'),
]
self.assertEqual(expected,found)
def test_search_fields_multivalue(self):
reader = BigBedReader(self.bb_indexed)
found = list(
reader.search("name", "should_have_no_match",
"should_also_have_no_match"))
self.assertEqual([], found)
found = list(reader.search("Name", "Sam-S-RE", "Sam-S-RK"))
expected = [
SegmentChain(GenomicSegment('2L', 106902, 107000, '+'),
GenomicSegment('2L', 107764, 107838, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RE', 'CG2674-RE']'",
ID='FBtr0089437',
Name='Sam-S-RE',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107760, 107838, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 111337, '+'),
Alias='na',
ID='FBtr0308091',
Name='Sam-S-RK',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='110900',
thickstart='108685',
type='exon'),
]
self.assertEqual(expected, found)
def test_search_fields_singlevalue(self):
reader = BigBedReader(self.bb_indexed)
found = list(reader.search("name", "should_have_no_match"))
self.assertEqual([], found)
found = list(reader.search("Name", "Sam-S-RE"))
expected = [
SegmentChain(GenomicSegment('2L', 106902, 107000, '+'),
GenomicSegment('2L', 107764, 107838, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RE', 'CG2674-RE']'",
ID='FBtr0089437',
Name='Sam-S-RE',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
]
self.assertEqual(expected, found)
found = list(reader.search("gene_id", "FBgn0005278"))
expected = [
SegmentChain(GenomicSegment('2L', 106902, 107000, '+'),
GenomicSegment('2L', 107764, 107838, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RE', 'CG2674-RE']'",
ID='FBtr0089437',
Name='Sam-S-RE',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107760, 107838, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 111337, '+'),
Alias='na',
ID='FBtr0308091',
Name='Sam-S-RK',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='110900',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107760, 107838, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111004, 111117, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114210, '+'),
Alias="'['M(2)21AB-RB', 'CG2674-RB']'",
ID='FBtr0089428',
Name='Sam-S-RB',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='112741',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107760, 107838, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RA', 'CG2674-RA']'",
ID='FBtr0089429',
Name='Sam-S-RA',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107760, 107956, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias='na',
ID='FBtr0330656',
Name='Sam-S-RL',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='112781',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107936, 108226, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114210, '+'),
Alias="'['M(2)21AB-RH', 'CG2674-RH']'",
ID='FBtr0089432',
Name='Sam-S-RH',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107936, 108101, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RD', 'CG2674-RD']'",
ID='FBtr0089430',
Name='Sam-S-RD',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 107936, 108101, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111004, 111117, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RC', 'CG2674-RC']'",
ID='FBtr0089431',
Name='Sam-S-RC',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 108088, 108226, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RF', 'CG2674-RF']'",
ID='FBtr0089433',
Name='Sam-S-RF',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 108132, 108346, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111906, 112019, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RI', 'CG2674-RI']'",
ID='FBtr0089434',
Name='Sam-S-RI',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 108132, 108226, '+'),
GenomicSegment('2L', 108587, 108809, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111004, 111117, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114432, '+'),
Alias="'['M(2)21AB-RJ', 'CG2674-RJ']'",
ID='FBtr0089435',
Name='Sam-S-RJ',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='108685',
type='exon'),
SegmentChain(GenomicSegment('2L', 109593, 109793, '+'),
GenomicSegment('2L', 110405, 110483, '+'),
GenomicSegment('2L', 110754, 110877, '+'),
GenomicSegment('2L', 111004, 111117, '+'),
GenomicSegment('2L', 112689, 113369, '+'),
GenomicSegment('2L', 113433, 114210, '+'),
Alias="'['M(2)21AB-RG', 'CG2674-RG']'",
ID='FBtr0089436',
Name='Sam-S-RG',
color='#000000',
gene_id='FBgn0005278',
score='0.0',
thickend='113542',
thickstart='109750',
type='exon'),
]
self.assertEqual(sorted(expected), sorted(found))