def test_goodFiles(tmpdir, bamFile):
d = tmpdir.mkdir('dir')
p = d.join('test.bam')
header = {'HD': {'VN': '1.0'}, 'SQ': [{'LN': 1000, 'SN': 'ref'}]}
outFile = pysam.AlignmentFile(str(p), "wb", header=header)
a = pysam.AlignedSegment()
a.query_name = "read1"
a.query_sequence = "AAAAATTTTT"
a.reference_id = 0
a.reference_start = 32
a.mapping_quality = 20
a.cigar = ((0, 10), )
#a.query_qualities = pysam.qualitystring_to_array("((((((((((")
outFile.write(a)
outFile.close()
pysam.index(str(p))
count = 0
out = next(getstartends.getStartsInFile(str(p)))
assert out['start'] == 33
assert out['end'] == 42
assert out['strand'] == '+'
assert out['ref'] == 'ref'
for read, start, strand, end in zip(
getstartends.getStartsInFile(str(bamFile), maxGaps=10),
[29, 33, 33], ['-', '+', '+'], [38, 42, 46]):
assert read['start'] == start
assert read['strand'] == strand
assert read['end'] == end
for read, start, strand, end in zip(
getstartends.getStartsInFile(str(bamFile)), [29, 33], ['-', '+'],
[38, 42]):
assert read['start'] == start
assert read['strand'] == strand
assert read['end'] == end
def test_badFiles(tmpdir):
d = tmpdir.mkdir('dir')
p = d.join('test.txt')
with pytest.raises(ValueError):
next(getstartends.getStartsInFile(str(d)))
#doesn't exist yet
with pytest.raises(IOError):
next(getstartends.getStartsInFile(str(p)))
#incorrectly formatted file
p.write("test")
with pytest.raises(ValueError):
next(getstartends.getStartsInFile(str(p)))
#make unreadable
os.chmod(str(p), os.stat(str(p)).st_mode & ~stat.S_IREAD)
with pytest.raises(ValueError):
next(getstartends.getStartsInFile(str(p)))
def test_main(capsys, tmpdir, bamFile):
with pytest.raises(SystemExit):
getstartends.main()
out, err = capsys.readouterr()
assert 'usage' in err
with pytest.raises(SystemExit):
getstartends.main(['-h'])
out, err = capsys.readouterr()
assert 'usage' in out
getstartends.main(['-v', str(bamFile)])
out, err = capsys.readouterr()
assert 'Arguments' in err
compare = getstartends.getStartsInFile(str(bamFile))
count = 0
for ii, jj in zip(out.split('\n')[1:], compare):
ii = ii.split(',')
count += 1
assert ii[0] == jj['ref']
assert int(ii[1]) == jj['start']
assert int(ii[2]) == jj['end']
assert ii[3] == jj['strand']
assert count == 2
compare = getstartends.getStartsInFile(str(bamFile), maxGaps=10)
getstartends.main([str(bamFile), '-g 10'])
out, err = capsys.readouterr()
count = 0
for ii, jj in zip(out.split('\n')[1:], compare):
count += 1
ii = ii.split(',')
assert ii[0] == jj['ref']
assert int(ii[1]) == jj['start']
assert int(ii[2]) == jj['end']
assert ii[3] == jj['strand']
assert count == 3
getstartends.main([str(bamFile), '-g 10', '-n'])
noHead, err = capsys.readouterr()
for ii, jj in zip(out.split('\n')[1:], noHead.split('\n')):
assert ii == jj
getstartends.main([str(bamFile), '-g 10', '-n', '-c'])
regCol, err = capsys.readouterr()
for ii, jj in zip(out.split('\n')[1:], regCol.split('\n')):
if ii:
ii = "None," + ii
assert ii == jj
getstartends.main([str(bamFile), '-g 10', '-n', '-c', '-r', 'ref:1-100'])
regCol, err = capsys.readouterr()
for ii, jj in zip(out.split('\n')[1:], regCol.split('\n')):
if ii:
ii = "ref:1-100," + ii
assert ii == jj
d = tmpdir.mkdir('dir')
p = d.join('test.regions')
p.write("ref:1-10\nref:1-100")
getstartends.main([str(bamFile), '-g 10', '-n', '-c', '-f', str(p)])
fileOut, err = capsys.readouterr()
for ii, jj in zip(regCol.split('\n'), fileOut.split('\n')):
assert ii == jj
