def test_m80_init(m80_Fasta):
'''
Test init from a m80 object.
Needs to inherit from m80_Fasta,
but dont use it directly, use the m80
API instead
'''
# grab from mm80
f = lp.Fasta('ACGT')
assert len(f['chr1']) == 100
def test_chrom_attrs(smpl_fasta, m80_Fasta):
c1 = smpl_fasta['chr1']
assert 'foobar' in c1._attrs
c2 = lp.Fasta('ACGT')
assert 'foo' in c2['chr1']._attrs
import os
import minus80 as m80
import locuspocus as lp
from minus80.RawFile import RawFile
ids = dict()
with open('ensemble_id_map.txt','r') as IN:
for line in IN:
i,j = line.strip().split()
ids[i] = j
if m80.Tools.available('EquCab3',dtype='Fasta'):
ec3 = lp.Fasta('EquCab3')
else:
ec3 = lp.Fasta.from_file('EquCab3','EquCab3.fa.gz')
if not os.path.exists('EquCab3_nice.fasta'):
with open('EquCab3_nice.fasta','w') as OUT:
for chrom_name in ec3.chrom_names():
print(f'Printing out {chrom_name}')
chrom = ec3[chrom_name]
# try to get easy_id
if chrom_name in ids:
chrom_name = f"{ids[chrom_name]} {chrom_name}"
# Keep track of lengths
start_length = len(chrom)
printed_length = 0
# Loop and print
print(f'>{chrom_name} {" ".join(chrom._attrs)}',file=OUT)
for i in range(0,len(chrom),70):
sequence = chrom.seq[i:i+70]