def test_fromgff3():
features = fromgff3(plasmodb_gff3_file.name)
expect_header = ('seqid', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase', 'attributes')
eq_(expect_header, header(features))
# apidb|MAL1 ApiDB supercontig 1 643292 . + . ID=apidb|MAL1;Name=MAL1;description=MAL1;size=643292;web_id=MAL1;molecule_type=dsDNA;organism_name=Plasmodium falciparum;translation_table=11;topology=linear;localization=nuclear;Dbxref=ApiDB_PlasmoDB:MAL1,GenBank:NC_004325,taxon:36329
row = list(features)[1]
eq_('apidb|MAL1', row[0])
eq_('ApiDB', row[1])
eq_('supercontig', row[2])
eq_(1, row[3])
eq_(643292, row[4])
eq_('.', row[5])
eq_('+', row[6])
eq_('.', row[7])
eq_('apidb|MAL1', row[8]['ID'])
eq_('MAL1', row[8]['Name'])
eq_('Plasmodium falciparum', row[8]['organism_name'])
# test data wrapped in hybrid rows
eq_('apidb|MAL1', row['seqid'])
eq_('ApiDB', row['source'])
eq_('supercontig', row['type'])
eq_(1, row['start'])
eq_(643292, row['end'])
eq_('.', row['score'])
eq_('+', row['strand'])
eq_('.', row['phase'])
eq_('apidb|MAL1', row['attributes']['ID'])
eq_('MAL1', row['attributes']['Name'])
eq_('Plasmodium falciparum', row['attributes']['organism_name'])
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])
def test_fromgff3_trailing_semicolon():
features = fromgff3(plasmodb_gff3_file.name)
#apidb|MAL2 ApiDB supercontig 1 947102 . + . ID=apidb|MAL2;Name=MAL2;description=MAL2;size=947102;web_id=MAL2;molecule_type=dsDNA;organism_name=Plasmodium falciparum;translation_table=11;topology=linear;localization=nuclear;Dbxref=ApiDB_PlasmoDB:MAL2,GenBank:NC_000910,taxon:36329;
row = list(features)[2]
eq_('apidb|MAL2', row[0])
eq_('ApiDB', row[1])
eq_('supercontig', row[2])
eq_(1, row[3])
eq_(947102, row[4])
eq_('.', row[5])
eq_('+', row[6])
eq_('.', row[7])
eq_('apidb|MAL2', row[8]['ID'])
eq_('MAL2', row[8]['Name'])
eq_('Plasmodium falciparum', row[8]['organism_name'])
strand TEXT NOT NULL,
alias TEXT,
description TEXT,
fulltext TEXT,
CONSTRAINT name_pk PRIMARY KEY (name)
)
"""
conn = sqlite3.connect('db.sqlite3')
conn.execute('PRAGMA legacy_file_format=false') # needed otherwise index sort order is ignored
log('drop gene table')
conn.execute('DROP TABLE IF EXISTS gene')
log('create gene table')
conn.execute(schema)
log('prepare the data for loading')
gff = fromgff3('Pfalciparum_PlasmoDB-7.2.gff')
# select only genes
t0 = selecteq(gff, 'type', 'gene')
# columns from attributes
t1 = unpackdict(t0, 'attributes', keys=('ID', 'Name', 'Alias', 'description'))
# add a 'chromosome' column with MAL.. style naming
def mk_chromosome(row):
seqid = row['seqid']
if seqid.startswith('apidb|Pf3D7_0'):
return 'MAL' + seqid[13:]
elif seqid.startswith('apidb|Pf3D7_'):
return 'MAL' + seqid[12:]
else:
return seqid
t2 = addfield(t1, 'chromosome', mk_chromosome)
# add a 'fulltext' column
def test_fromgff3_region():
tbl_features = fromgff3('fixture/sample.sorted.gff.gz', region='apidb|MAL5')
eq_(7, nrows(tbl_features))
tbl_features = fromgff3('fixture/sample.sorted.gff.gz', region='apidb|MAL5:1289593-1289595')
eq_(4, nrows(tbl_features))
