def test_auto_strand(self):
""" Test that --auto-strand produces the same output as --reverse --complement"""
with NamedTemporaryFile() as auto_strand:
with NamedTemporaryFile() as noto_strand:
main(['--auto-strand', '-o', auto_strand.name, 'data/genes.fasta', 'gi|557361099|gb|KF435150.1|:100-1'])
main(['--reverse', '--complement', '-o', noto_strand.name, 'data/genes.fasta', 'gi|557361099|gb|KF435150.1|:1-100'])
print(auto_strand.read())
print()
print(noto_strand.read())
self.assertTrue(filecmp.cmp(auto_strand.name, noto_strand.name))
def test_auto_strand(self):
""" Test that --auto-strand produces the same output as --reverse --complement"""
with NamedTemporaryFile() as auto_strand:
with NamedTemporaryFile() as noto_strand:
main([
'--auto-strand', '-o', auto_strand.name,
'data/genes.fasta', 'gi|557361099|gb|KF435150.1|:100-1'
])
main([
'--reverse', '--complement', '-o', noto_strand.name,
'data/genes.fasta', 'gi|557361099|gb|KF435150.1|:1-100'
])
print(auto_strand.read())
print()
print(noto_strand.read())
self.assertTrue(filecmp.cmp(auto_strand.name,
noto_strand.name))
def test_fetch_whole_file(self):
main(['data/genes.fasta'])
def test_short_line_lengths(self):
main(['data/genes.fasta', '--bed', 'data/malformed.bed'])
def test_not_regexp_multi(self):
main(['data/genes.fasta', '-g', 'XR', '-g', 'XM', '-v'])
def test_regexp(self):
main(['data/genes.fasta', '-g', 'XR'])
def test_not_regexp_multi(self):
main(['data/genes.fasta', '-g', 'XR', '-g', 'XM', '-v'])
def test_regexp(self):
main(['data/genes.fasta', '-g', 'XR'])
def test_key_warning(self):
main(['data/genes.fasta', 'foo'])
def test_fetch_error(self):
main(['data/genes.fasta', 'gi|557361099|gb|KF435150.1|:1-1000'])
def test_split_entry(self):
main(['--split-files', 'data/genes.fasta', 'gi|557361099|gb|KF435150.1|'])
assert os.path.exists('gi557361099gbKF435150.1.fasta')
os.remove('gi557361099gbKF435150.1.fasta')
def test_fetch_whole_file(self):
main(['data/genes.fasta'])
def test_short_line_lengths(self):
main(['data/genes.fasta', '--bed', 'data/malformed.bed'])
from pyfaidx.cli import main
if __name__ == '__main__':
main()