Source code for outrigger.tests.io.test_star
import os
import pandas as pd
import pandas.util.testing as pdt
import pytest
import six
@pytest.fixture
[docs]def sj_out_tab(tmpdir):
s = """chr1 76 299 1 2 1 0 1 39
chr1 201 299 1 1 1 0 1 10
chr1 201 249 1 1 0 0 1 22
chr1 201 799 1 1 1 19 20 43
chr1 201 799 1 1 0 8 15 41
chr1 155832 164262 1 1 1 61 3 46
chr1 156087 156200 1 1 0 1 14 44
chr1 329977 334128 1 1 1 0 2 14
chr1 569184 569583 1 1 0 0 1 17
chr1 655581 659737 1 1 1 0 2 14
chr1 661725 662046 1 1 0 0 1 22
chr1 668587 671992 1 1 0 0 4 28
"""
df = pd.read_table(six.StringIO(s), header=None, sep='\s+')
filename = '{0}/SJ.out.tab'.format(tmpdir)
df.to_csv(filename, index=False, header=False, sep='\t')
return filename
[docs]def test_read_sj_out_tab(sj_out_tab, simulated_unprocessed):
from outrigger.io.star import read_sj_out_tab
test = read_sj_out_tab(sj_out_tab)
csv = os.path.join(simulated_unprocessed, 'true_splice_junctions.csv')
true = pd.read_csv(csv)
assert (test.junction_start < test.junction_stop).all()
pdt.assert_frame_equal(test, true)
[docs]def test_int_to_intron_motif():
from outrigger.io.star import int_to_junction_motif
ints = [0, 1, 2, 3, 4, 5, 6]
test = [int_to_junction_motif(i) for i in ints]
true = ['non-canonical', 'GT/AG', 'GT/AG', 'GC/AG', 'GC/AG', 'AT/AC',
'AT/AC']
assert test == true
@pytest.fixture
[docs]def splice_junction_csv(ignore_multimapping, tasic2016_intermediate):
"""Different file depending on whether multimapping is True"""
template = os.path.join(tasic2016_intermediate,
'index', 'star',
'splice_junctions_ignore_multimapping{}.csv')
return template.format(str(ignore_multimapping))
[docs]def test_read_multiple_sj_out_tab(sj_filenames, ignore_multimapping,
splice_junction_csv):
from outrigger.io.star import read_multiple_sj_out_tab
from outrigger.common import READS
# Read csv file and convert to numeric
true = pd.read_csv(splice_junction_csv)
true = true.convert_objects()
test = read_multiple_sj_out_tab(
sj_filenames, ignore_multimapping=ignore_multimapping)
assert READS in test
pdt.assert_frame_equal(test, true)
