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#!/usr/bin/env python
"""Unit tests for Mage format writer.
"""
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.util.table import Table
from cogent.format.bedgraph import get_header
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
from cogent.util.unit_test import TestCase, main
class FormatBedgraph(TestCase):
def test_only_required_columns(self):
"""generate bedgraph from minimal data"""
table = Table(header=['chrom', 'start', 'end', 'value'],
rows=[['1', 100, i, 0] for i in range(101,111)] + \
[['1', 150, i, 10] for i in range(151,161)])
bgraph = table.tostring(format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0))
self.assertTrue(bgraph,
'\n'.join(['track type=bedGraph name="test track" '\
+'description="test of bedgraph" color=255,0,0',
'1\t100\t110\t0', '1\t150\t160\t10']))
def test_merged_overlapping_spans(self):
"""bedgraph merged overlapping spans, one chrom"""
rows = [['1', i, i+1, 0] for i in range(100, 121)] +\
[['1', i, i+1, 10] for i in range(150, 161)]
table = Table(header=['chrom', 'start', 'end', 'value'], rows=rows)
bgraph = table.tostring(format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0))
self.assertTrue(bgraph,
'\n'.join(['track type=bedGraph name="test track" '\
+'description="test of bedgraph" color=255,0,0',
'1\t100\t120\t0', '1\t150\t160\t10']))
def test_merged_overlapping_spans_multichrom(self):
"""bedgraph merged overlapping spans, two crhoms"""
rows = [['1', i, i+1, 0] for i in range(100, 121)] +\
[['1', i, i+1, 10] for i in range(150, 161)]
rows += [['2', i, i+1, 0] for i in range(100, 121)]
table = Table(header=['chrom', 'start', 'end', 'value'], rows=rows)
bgraph = table.tostring(format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0))
self.assertTrue(bgraph,
'\n'.join(['track type=bedGraph name="test track" '\
+'description="test of bedgraph" color=255,0,0',
'1\t100\t120\t1', '1\t150\t160\t10', '2\t105\t120\t1',]))
def test_invalid_args_fail(self):
"""incorrect bedgraph args causes RuntimeError"""
rows = [['1', i, i+1, 0] for i in range(100, 121)] +\
[['1', i, i+1, 10] for i in range(150, 161)]
table = Table(header=['chrom', 'start', 'end', 'value'], rows=rows)
self.assertRaises(RuntimeError, table.tostring,
format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0), abc=None)
def test_invalid_table_fails(self):
"""assertion error if table has > 4 columns"""
rows = [['1', i, i+1, 0, 1] for i in range(100, 121)] +\
[['1', i, i+1, 10, 1] for i in range(150, 161)]
table = Table(header=['chrom', 'start', 'end', 'value', 'blah'],
rows=rows)
self.assertRaises(AssertionError, table.tostring,
format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0), abc=None)
def test_boolean_correctly_formatted(self):
"""boolean setting correctly formatted"""
rows = [['1', i, i+1, 0] for i in range(100, 121)] +\
[['1', i, i+1, 10] for i in range(150, 161)]
table = Table(header=['chrom', 'start', 'end', 'value'], rows=rows)
bgraph = table.tostring(format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0), autoScale=True)
self.assertTrue(bgraph,
'\n'.join(['track type=bedGraph name="test track" '\
+'description="test of bedgraph" color=255,0,0 autoScale=on',
'1\t100\t110\t1', '1\t150\t160\t10']))
def test_int_correctly_formatted(self):
"""int should be correctly formatted"""
rows = [['1', i, i+1, 0] for i in range(100, 121)] +\
[['1', i, i+1, 10] for i in range(150, 161)]
table = Table(header=['chrom', 'start', 'end', 'value'], rows=rows)
bgraph = table.tostring(format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0), smoothingWindow=10)
self.assertTrue(bgraph,
'\n'.join(['track type=bedGraph name="test track" '\
+'description="test of bedgraph" color=255,0,0 smoothingWindow=10',
'1\t100\t110\t1', '1\t150\t160\t10']))
def test_raises_on_incorrect_format_val(self):
"""raise AssertionError when provide incorrect format value"""
rows = [['1', i, i+1, 0] for i in range(100, 121)] +\
[['1', i, i+1, 10] for i in range(150, 161)]
table = Table(header=['chrom', 'start', 'end', 'value'], rows=rows)
self.assertRaises(AssertionError, table.tostring,
format='bedgraph', name='test track',
description='test of bedgraph', color=(255,0,0),
windowingFunction='sqrt')
if __name__ == '__main__':
main()
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