def test_from_2_to_3():
'It tests that we can go from gff2 to gff3'
GFF2 = '''Chrctg0\tassembly\tChromosome\t1\t140722177\t.\t.\t.\tSequence "Chrctg0"; Name "Chrctg0"
Chrctg0\tFPC\tcontig\t1\t140722177\t.\t.\t.\tcontig "ctg0"; Name "ctg0"
Chrctg0\tFPC\tBAC\t109076481\t109461505\t.\t.\t.\tBAC "Cm45_J09"; Name "Cm45_J09"; Contig_hit "0"
Chrctg0\tFPC\tBAC\t97189889\t97329153\t.\t.\t.\tBAC "Cm40_O16 3"; Name "Cm40_O16"; Contig_hit "0"
Chrctg0\tFPC\tBAC\t57982977\t58302465\t.\t.\t.\tBAC "Cm22_F20"; Name "Cm22_F20"; Contig_hit "0"
Chrctg0\tFPC\tBAC\t57982978\t58302466\t.\t.\t.\tBAC "Cm22_F20"; Name "Cm22_F20"; Contig_hit "0"
'''
inh = NamedTemporaryFile()
inh.write(GFF2)
inh.flush()
in_gff = GffFile(inh.name)
outh = NamedTemporaryFile()
write_gff(outh.name, in_gff.items)
result = outh.read()
assert 'ID=Cm22_F20_2' in result
assert 'BAC=Cm40_O16%203' in result
def cmap_to_gff(data, fhand):
'Given a dict with the cmap data and an output fhand it writes a gff3 file'
gff = []
gff.append((METADATA, 'cmap-gff-version 1'))
# This marker count is used where there is a markers in two maps.
marker_count = {}
marker_id_map = {}
for mapset in data['map_sets']:
species_name = mapset['species']
species = data['species'][species_name]
gff.append(_species_pragma(species))
gff.append((METADATA, '#'))
gff.append(_map_set_pragma(mapset))
features_in_mapset = set()
for map_ in mapset['maps']:
#start and end
start = None
end = None
for feat_loc in map_['feature_locations']:
this_start = feat_loc['start']
if 'end' in feat_loc:
this_end = feat_loc['end']
else:
this_end = feat_loc['start']
if start is None or start > this_start:
start = this_start
if end is None or end < this_end:
end = this_end
map_['start'] = start
map_['end'] = end
gff.extend(_map_pragma(map_, mapset['accession']))
gff.extend(_map_features(map_, data['features'],
mapset['accession'], marker_count,
marker_id_map,
features_in_mapset))
#the correspondences
gff.extend(_cmap_correspondences(marker_count, marker_id_map))
write_gff(fhand.name, gff)
def test_simple_output():
'We can write a simple gff3 file'
feat1 = {'seqid': 'ctg123',
'type': 'gene',
'start': 1000,
'end': 9000,
#'id': 'gene00001',
#'name': 'EDEN',
'attributes':{'ID':'gene00001', 'Name':'EDEN'}
}
feats = [(METADATA, 'sequence-region ctg123 1 1497228'),
(FEATURE, feat1)]
result = '''##gff-version 3
##sequence-region ctg123 1 1497228
ctg123\t.\tgene\t1000\t9000\t.\t.\t.\tID=gene00001;Name=EDEN\n'''
outh = NamedTemporaryFile()
write_gff(outh.name, feats)
assert outh.read() in result
feat1 = {'id':'23',
'seqid': 'ctg123',
'type': 'gene',
'start': 1000,
'end': 9000,
'name': 'hola',
'attributes' : {'Parent': ['p1', 'p2']}}
feats = [(FEATURE, feat1)]
outh = NamedTemporaryFile()
write_gff(outh.name, feats)
result = outh.read()
expected = '##gff-version 3\nctg123\t.\tgene\t1000\t9000\t.\t.\t.\t'
assert expected in result
assert 'Name=hola' in result
#escaping some caracteres
feat1 = {'id':'23',
'seqid': 'ctg123',
'type': 'gene',
'start': 1000,
'end': 9000,
'name': 'hola',
'attributes':{'Dbxref':'peoi%25l a%20k%s'}}
feats = [(FEATURE, feat1)]
outh = NamedTemporaryFile()
write_gff(outh.name, feats)
result = outh.read()
assert 'Dbxref=peoi%25l%20a%20k%25s' in result
