def m80_Fasta():
'''
Create a Fasta which doesn't get
returned. Access the Fasta through
the m80 API
'''
# delete the onl
m80tools.delete('Fasta','ACGT',force=True)
f = Fasta.from_file('ACGT','raw/ACGT.fasta')
return True
def testRefGen():
# We have to build it
if m80tools.available('RefLoci', 'Zm5bFGS'):
x = RefLoci('Zm5bFGS')
else:
m80tools.delete('RefLoci', 'Zm5bFGS', force=True)
gff = os.path.expanduser(os.path.join('raw', 'ZmB73_5b_FGS.gff.gz'))
x = RefLoci('Zm5bFGS')
if len(x) == 0:
x.import_gff(gff)
x.set_primary_feature_type('gene')
return x
def simpleRefLoci():
m80tools.delete('RefLoci','simpleRefLoci',force=True)
# Create a Locus
a = Locus(1,100,150, id='gene_a')
# Create a couple more!
b = Locus(1,160,175, id='gene_b')
c = Locus(1,180,200, id='gene_c')
d = Locus(1,210,300, id='gene_d')
e = Locus(2,100,150, id='gene_e')
x = RefLoci('simpleRefLoci')
x.add_loci([a,b,c,d,e])
return x
def testRefGen():
# We have to build it
m80tools.delete('RefLoci','Zm5bFGS',force=True)
gff = os.path.expanduser(
os.path.join(
'raw', 'ZmB73_5b_FGS.gff.gz'
)
)
x = RefLoci('Zm5bFGS')
if len(x) == 0:
x.add_gff(
gff
)
return x
def smpl_fasta():
''' A simple fasta that agrees with smpl_annot'''
m80tools.delete('Fasta','smpl_fasta',force=True)
fasta = Fasta('smpl_fasta')
chr1 = Chromosome('chr1','A'*500000)
chr2 = Chromosome('chr2','C'*500000)
chr3 = Chromosome('chr3','G'*500000)
chr4 = Chromosome('chr4','T'*500000)
fasta.add_chrom(chr1)
fasta.add_chrom(chr2)
fasta.add_chrom(chr3)
fasta.add_chrom(chr4)
fasta._add_nickname('chr1','CHR1')
fasta._add_attribute('chr1','foobar')
return fasta