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#!/usr/bin/env python
# test_sffinfo.py
import os
import shutil
import tempfile
from cogent.util.unit_test import TestCase, main
from cogent.app.util import ApplicationError
from cogent.app.sffinfo import (
ManyValuedParameter, Sffinfo, sffinfo_from_file)
__author__ = "Kyle Bittinger"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Kyle Bittinger"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
__status__ = "Prototype"
class ManyValuedParameterTests(TestCase):
def test_init(self):
"""__init__() should set appropriate class variables."""
p = ManyValuedParameter(None, None)
self.assertEqual(p.Name, None)
self.assertEqual(p.Value, None)
self.assertEqual(p.Delimiter, None)
self.assertEqual(p.Quote, None)
p = ManyValuedParameter('-', 'a', Values=['abc'])
self.assertEqual(p.Value, ['abc'])
def test_append(self):
"""append() should append values to Value class attribute."""
p = ManyValuedParameter(None, None)
p.append('abc')
p.append(3)
self.assertEqual(p.Value, ['abc', 3])
def test_on(self):
"""on() should alias append()."""
p = ManyValuedParameter(None, None)
p.on('abc')
p.on(3)
self.assertEqual(p.Value, ['abc', 3])
def test_str(self):
"""__str__() should produce quoted, delimited string of parameter values."""
p = ManyValuedParameter(None, None)
p.append('abc')
p.append(3)
self.assertEqual(str(p), 'abc3')
p = ManyValuedParameter(None, None, Quote='"', ValueDelimiter=',')
p.append('abc')
p.append(3)
self.assertEqual(str(p), '"abc","3"')
class SffinfoTests(TestCase):
def setUp(self):
test_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
self.sff_fp = os.path.join(test_dir, 'data', 'test.sff')
def test_base_command(self):
"""BaseCommand should include non-positional parameters."""
s = Sffinfo()
expected = 'cd "%s/"; sffinfo' % os.getcwd()
self.assertEqual(s.BaseCommand, expected)
s.Parameters['-a'].on()
expected = 'cd "%s/"; sffinfo -a' % os.getcwd()
self.assertEqual(s.BaseCommand, expected)
# accession number parameters should not be included in base command
s.Parameters['-a'].off()
s.Parameters['accno'].on('12345ABC')
expected = 'cd "%s/"; sffinfo' % os.getcwd()
self.assertEqual(s.BaseCommand, expected)
def test_changing_working_dir(self):
"""WorkingDir should be created and included in BaseCommand."""
# Directory is not created, only filename is returned
working_dir = tempfile.mktemp()
self.assertRaises(OSError, os.rmdir, working_dir)
a = Sffinfo(WorkingDir=working_dir)
expected = 'cd "%s/"; sffinfo' % working_dir
self.assertEqual(a.BaseCommand, expected)
# Removing the directory is proof that it was created. If the
# directory is not there, an OSError will be raised.
os.rmdir(working_dir)
def test_input_handler(self):
"""Sffinfo should decorate input handler output with accession numbers"""
my_accno = '12345ABC'
a = Sffinfo()
a.Parameters['accno'].on(my_accno)
self.assertEqual(a.InputHandler, '_input_handler_decorator')
observed = getattr(a, a.InputHandler)(self.sff_fp)
expected = '"%s" %s' % (self.sff_fp, my_accno)
self.assertEqual(observed, expected)
def test_call(self):
"""Simple sffinfo call should produce expected output."""
a = Sffinfo()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, sffinfo_output)
def test_call_with_accno(self):
"""Sffinfo accession number parameters should filter output."""
# Valid accession number
a = Sffinfo()
a.Parameters['accno'].on('FA6P1OK01CGMHQ')
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, sffinfo_output)
# Invalid accession number
a = Sffinfo()
a.Parameters['accno'].on('AAAAAAAAAAAAAA')
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, empty_sffinfo_output)
def test_call_with_flags(self):
"""Sffinfo flags should alter output as expected."""
# -a flag
a = Sffinfo()
a.Parameters['-a'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
self.assertEqual(observed, 'FA6P1OK01CGMHQ\n')
# -s flag
a = Sffinfo()
a.Parameters['-s'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
expected = (
'>FA6P1OK01CGMHQ length=48 xy=0892_1356 region=1 '
'run=R_2008_05_28_17_11_38_\n'
'ATCTGAGCTGGGTCATAGCTGCCTCCGTAGGAGGTGCCTCCCTACGGC\n'
)
self.assertEqual(observed, expected)
# -q flag
a = Sffinfo()
a.Parameters['-q'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
expected = (
'>FA6P1OK01CGMHQ length=48 xy=0892_1356 region=1 '
'run=R_2008_05_28_17_11_38_\n'
'32 32 32 32 32 32 32 25 25 21 21 21 28 32 32 31 30 30 32 32 32 '
'33 31 25 18 18 20 18 32 30 28 23 22 22 24 28 18 19 18 16 16 16 '
'17 18 13 17 27 21\n')
self.assertEqual(observed, expected)
# -f flag
a = Sffinfo()
a.Parameters['-f'].on()
app_results = a(self.sff_fp)
observed = app_results['StdOut'].read()
expected = (
'>FA6P1OK01CGMHQ xy=0892_1356 region=1 run=R_2008_05_28_17_11_38_\n'
'A,1.02 C,0.00 G,0.00 T,0.99 A,0.00 C,1.00 G,0.00 T,1.00 A,0.00 C,0.00\n'
'G,1.00 T,0.00 A,1.10 C,0.00 G,1.08 T,0.00 A,0.00 C,1.46 G,0.00 T,0.88\n'
'A,0.18 C,0.00 G,2.69 T,1.01 A,0.08 C,0.96 G,0.00 T,0.02 A,0.92 C,0.08\n'
'G,0.00 T,0.98 A,0.68 C,0.00 G,0.89 T,0.00 A,0.00 C,1.15 G,0.00 T,1.13\n'
'A,0.00 C,0.02 G,1.12 T,0.05 A,0.15 C,1.84 G,0.00 T,1.10 A,0.00 C,2.47\n'
'G,0.96 T,0.86 A,1.06 C,0.00 G,1.96 T,0.12 A,0.93 C,0.13 G,1.65 T,1.06\n'
'A,0.06 C,0.00 G,0.99 T,0.00 A,0.00 C,1.87 G,0.44 T,1.08 A,0.00 C,3.25\n'
'G,0.09 T,0.97 A,0.50 C,1.00 G,1.72 T,0.07 A,0.00 C,0.92 \n')
self.assertEqual(observed, expected)
class SffinfoFunctionTests(TestCase):
def test_sffinfo_from_file(self):
"""sffinfo_from_file should return file object with sffinfo output."""
test_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sff_fp = os.path.join(test_dir, 'data', 'test.sff')
observed = sffinfo_from_file(sff_fp).read()
self.assertEqual(observed, sffinfo_output)
sffinfo_output = '''Common Header:
Magic Number: 0x2E736666
Version: 0001
Index Offset: 1504
Index Length: 706
# of Reads: 1
Header Length: 440
Key Length: 4
# of Flows: 400
Flowgram Code: 1
Flow Chars: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
Key Sequence: TCAG
>FA6P1OK01CGMHQ
Run Prefix: R_2008_05_28_17_11_38_
Region #: 1
XY Location: 0892_1356
Run Name: R_2008_05_28_17_11_38_FLX02070135_adminrig_KnightLauber
Analysis Name: /data/2008_05_28/R_2008_05_28_17_11_38_FLX02070135_adminrig_KnightLauber/D_2008_05_28_21_13_06_FLX02070135_KnightLauber_FullAnalysisAmplicons
Full Path: /data/2008_05_28/R_2008_05_28_17_11_38_FLX02070135_adminrig_KnightLauber/D_2008_05_28_21_13_06_FLX02070135_KnightLauber_FullAnalysisAmplicons/../D_2008_05_29_13_52_01_FLX02070135_Knight_Lauber_jones_SignalProcessingAmplicons
Read Header Len: 32
Name Length: 14
# of Bases: 77
Clip Qual Left: 5
Clip Qual Right: 52
Clip Adap Left: 0
Clip Adap Right: 0
Flowgram: 1.04 0.00 1.01 0.00 0.00 0.96 0.00 1.02 0.00 1.02 0.00 0.00 0.99 0.00 1.00 0.00 1.00 0.00 0.00 1.00 0.00 1.10 0.00 1.08 0.00 0.00 1.46 0.00 0.88 0.18 0.00 2.69 1.01 0.08 0.96 0.00 0.02 0.92 0.08 0.00 0.98 0.68 0.00 0.89 0.00 0.00 1.15 0.00 1.13 0.00 0.02 1.12 0.05 0.15 1.84 0.00 1.10 0.00 2.47 0.96 0.86 1.06 0.00 1.96 0.12 0.93 0.13 1.65 1.06 0.06 0.00 0.99 0.00 0.00 1.87 0.44 1.08 0.00 3.25 0.09 0.97 0.50 1.00 1.72 0.07 0.00 0.92 0.58 0.00 0.00 0.59 0.06 0.11 0.09 0.07 0.06 0.16 0.00 0.24 0.03 0.00 0.12 0.06 0.16 0.00 0.18 0.00 0.00 0.14 0.00 0.15 0.00 0.18 0.00 0.03 0.14 0.03 0.13 0.01 0.19 0.00 0.02 0.33 0.05 0.00 0.16 0.10 0.35 0.01 0.21 0.04 0.09 0.18 0.13 0.19 0.00 0.10 0.51 0.26 0.00 0.23 0.19 0.27 0.01 0.29 0.05 0.14 0.17 0.16 0.18 0.27 0.09 0.26 0.10 0.18 0.23 0.15 0.22 0.13 0.37 0.11 0.11 0.26 0.59 0.14 0.06 0.33 0.34 0.26 0.05 0.27 0.44 0.19 0.10 0.35 0.27 0.15 0.34 0.28 0.45 0.14 0.16 0.34 0.27 0.12 0.07 0.25 0.18 0.12 0.04 0.23 0.16 0.12 0.05 0.20 0.16 0.11 0.03 0.21 0.16 0.10 0.02 0.21 0.16 0.12 0.02 0.20 0.15 0.10 0.02 0.23 0.15 0.11 0.02 0.22 0.14 0.09 0.02 0.20 0.13 0.09 0.01 0.19 0.13 0.08 0.02 0.17 0.12 0.08 0.03 0.17 0.09 0.08 0.01 0.14 0.09 0.07 0.01 0.15 0.09 0.06 0.01 0.13 0.08 0.06 0.00 0.13 0.08 0.05 0.02 0.12 0.07 0.05 0.01 0.11 0.07 0.05 0.00 0.10 0.07 0.05 0.01 0.11 0.08 0.04 0.00 0.10 0.06 0.05 0.01 0.09 0.06 0.04 0.01 0.08 0.07 0.05 0.00 0.08 0.06 0.05 0.00 0.09 0.06 0.04 0.00 0.09 0.06 0.04 0.01 0.08 0.06 0.04 0.00 0.09 0.06 0.03 0.00 0.09 0.06 0.02 0.00 0.09 0.06 0.04 0.00 0.08 0.05 0.03 0.00 0.07 0.05 0.02 0.00 0.08 0.04 0.03 0.00 0.07 0.04 0.03 0.00 0.07 0.05 0.02 0.00 0.07 0.05 0.02 0.00 0.06 0.04 0.02 0.00 0.06 0.03 0.03 0.00 0.08 0.02 0.00 0.00 0.07 0.03 0.01 0.00 0.06 0.03 0.02 0.00 0.05 0.03 0.02 0.00 0.05 0.03 0.01 0.00 0.06 0.02 0.00 0.00 0.05 0.01 0.01 0.00 0.04 0.01 0.01 0.00 0.04 0.01 0.01 0.00 0.05 0.01 0.00 0.00 0.04 0.02 0.01 0.00 0.03 0.02 0.01 0.00 0.03 0.01 0.00 0.00 0.03 0.00 0.00 0.00 0.03 0.00 0.00 0.00 0.02 0.00
Flow Indexes: 1 3 6 8 10 13 15 17 20 22 24 27 29 32 32 32 33 35 38 41 42 44 47 49 52 55 55 57 59 59 60 61 62 64 64 66 68 68 69 72 75 75 77 79 79 79 81 82 83 84 84 87 88 91 102 126 130 138 140 145 153 157 161 164 166 171 175 179 183 187 191 195 199 203 211 215 219
Bases: tcagATCTGAGCTGGGTCATAGCTGCCTCCGTAGGAGGTGCCTCCCTACGGCgcnnnannnnngnnnnnnnnnnnnn
Quality Scores: 32 32 32 32 32 32 32 32 32 32 32 25 25 21 21 21 28 32 32 31 30 30 32 32 32 33 31 25 18 18 20 18 32 30 28 23 22 22 24 28 18 19 18 16 16 16 17 18 13 17 27 21 20 21 0 0 0 17 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0
'''
empty_sffinfo_output = '''Common Header:
Magic Number: 0x2E736666
Version: 0001
Index Offset: 1504
Index Length: 706
# of Reads: 1
Header Length: 440
Key Length: 4
# of Flows: 400
Flowgram Code: 1
Flow Chars: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
Key Sequence: TCAG
'''
if __name__ == '__main__':
main()
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