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#!/usr/bin/env python
"""tests for sff parser"""
__author__ = "Julia Goodrich, Jens Reeder"
__copyright__ = "Copyright 2009, The Cogent Project"
__credits__ = ["Julia Goodrich","Jens Reeder"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jens Reeder"
__email__ = "jreeder@colorado.edu"
__status__ = "Development"
from types import GeneratorType
from cogent.util.unit_test import TestCase, main
from cogent.parse.flowgram_parser import get_header_info, get_summaries,\
get_all_summaries, split_summary, parse_sff, lazy_parse_sff_handle
class SFFParserTests(TestCase):
"""Tests sff parser functions"""
def setUp(self):
"""Define some standard data"""
self.rec = """Common Header:
Magic Number: 0x2E736666
Version: 0001
Index Offset: 96099976
Index Length: 1158685
# of Reads: 57902
Header Length: 440
Key Length: 4
# of Flows: 400
Flowgram Code: 1
Flow Chars: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
Key Sequence: TCAG
>FIQU8OX05GCVRO
Run Prefix: R_2008_10_15_16_11_02_
Region #: 5
XY Location: 2489_3906
Run Name: R_2008_10_15_16_11_02_FLX04070166_adminrig_1548jinnescurtisstanford
Analysis Name: /data/2008_10_15/R_2008_10_15_16_11_02_FLX04070166_adminrig_1548jinnescurtisstanford/D_2008_10_15_15_12_26_FLX04070166_1548jinnescurtisstanford_FullAnalysis
Full Path: /data/2008_10_15/R_2008_10_15_16_11_02_FLX04070166_adminrig_1548jinnescurtisstanford/D_2008_10_15_15_12_26_FLX04070166_1548jinnescurtisstanford_FullAnalysis
Read Header Len: 32
Name Length: 14
# of Bases: 104
Clip Qual Left: 5
Clip Qual Right: 85
Clip Adap Left: 0
Clip Adap Right: 0
Flowgram: 1.06 0.08 1.04 0.08 0.05 0.94 0.10 2.01 0.10 0.07 0.96 0.09 1.04 1.96 1.07 0.10 1.01 0.13 0.08 1.01 1.06 1.83 2.89 0.18 0.96 0.13 0.99 0.11 1.94 0.12 0.13 1.92 0.21 0.07 0.94 0.17 0.03 0.97 2.76 0.15 0.05 1.02 1.14 0.10 0.98 2.54 1.13 0.96 0.15 0.21 1.90 0.16 0.07 1.78 0.22 0.07 0.93 0.22 0.97 0.08 2.02 0.15 0.19 1.02 0.19 0.09 1.02 0.17 0.99 0.09 0.18 1.84 0.16 0.91 0.10 1.10 1.00 0.20 0.09 1.11 3.01 1.07 1.98 0.14 0.22 1.09 0.17 1.99 0.15 0.20 0.92 0.17 0.07 1.01 2.96 0.15 0.07 1.06 0.20 1.00 0.10 0.12 1.00 0.15 0.08 1.90 0.19 0.10 0.99 0.18 0.09 0.99 1.08 0.15 0.07 1.06 0.14 1.84 0.13 0.11 0.95 1.05 0.13 1.04 1.10 0.18 0.94 0.14 0.10 0.97 1.08 0.12 1.08 0.18 0.08 1.00 0.13 0.98 0.15 0.87 0.13 0.19 1.01 3.06 0.17 0.11 1.04 0.09 1.03 0.10 0.11 2.02 0.16 0.11 1.04 0.04 0.09 1.87 0.13 2.09 0.13 0.10 0.97 0.17 0.08 0.08 0.04 0.12 0.05 0.08 0.07 0.08 0.05 0.07 0.06 0.07 0.03 0.05 0.04 0.09 0.04 0.07 0.04 0.07 0.06 0.03 0.06 0.06 0.06 0.06 0.07 0.09 0.04 0.05 0.08 0.05 0.04 0.09 0.06 0.03 0.02 0.08 0.04 0.06 0.05 0.08 0.03 0.08 0.05 0.05 0.05 0.10 0.05 0.05 0.07 0.06 0.04 0.06 0.05 0.03 0.04 0.05 0.06 0.04 0.04 0.07 0.04 0.04 0.05 0.05 0.04 0.07 0.06 0.05 0.03 0.08 0.05 0.06 0.04 0.06 0.05 0.04 0.04 0.04 0.05 0.06 0.04 0.05 0.04 0.05 0.05 0.06 0.05 0.06 0.04 0.06 0.07 0.06 0.05 0.05 0.05 0.06 0.06 0.04 0.05 0.06 0.03 0.06 0.04 0.06 0.05 0.03 0.06 0.06 0.05 0.06 0.04 0.03 0.06 0.06 0.06 0.03 0.04 0.05 0.05 0.07 0.04 0.05 0.06 0.07 0.07 0.05 0.07 0.06 0.05 0.06 0.05 0.07 0.06 0.05 0.06 0.07 0.05 0.06 0.04 0.06 0.05 0.05 0.06 0.04 0.06 0.04 0.03 0.06 0.05 0.05 0.04 0.05 0.05 0.04 0.04 0.05 0.06 0.06 0.04 0.04 0.05 0.06 0.04 0.04 0.04 0.05 0.05 0.04 0.05 0.05 0.03 0.06 0.06 0.06 0.04 0.07 0.05 0.05 0.04 0.06 0.06 0.05 0.05 0.07 0.04 0.06 0.06 0.06 0.04 0.06 0.03 0.06 0.04 0.06 0.04 0.09 0.05 0.05 0.05 0.07 0.06 0.05 0.05 0.06 0.05 0.05 0.05 0.04 0.04 0.06 0.05 0.05 0.05 0.05 0.04 0.05 0.05 0.06 0.04 0.05 0.05 0.05 0.05 0.05 0.04 0.06 0.04 0.05 0.05 0.04 0.05 0.05 0.05 0.04
Flow Indexes: 1 3 6 8 8 11 13 14 14 15 17 20 21 22 22 23 23 23 25 27 29 29 32 32 35 38 39 39 39 42 43 45 46 46 46 47 48 51 51 54 54 57 59 61 61 64 67 69 72 72 74 76 77 80 81 81 81 82 83 83 86 88 88 91 94 95 95 95 98 100 103 106 106 109 112 113 116 118 118 121 122 124 125 127 130 131 133 136 138 140 143 144 144 144 147 149 152 152 155 158 158 160 160 163
Bases: tcagGCTAACTGTAACCCTCTTGGCACCCACTAAACGCCAATCTTGCTGGAGTGTTTACCAGGCACCCAGCAATGTGAATAGTCActgagcgggctggcaaggc
Quality Scores: 37 37 37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 37 37 37 37 37 39 39 39 39 24 24 24 37 34 28 24 24 24 28 34 39 39 39 39 39 39 39 39 39 39 39 39 40 40 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37
>FIQU8OX05F8ILF
Run Prefix: R_2008_10_15_16_11_02_
Region #: 5
XY Location: 2440_0913
Run Name: R_2008_10_15_16_11_02_FLX04070166_adminrig_1548jinnescurtisstanford
Analysis Name: /data/2008_10_15/R_2008_10_15_16_11_02_FLX04070166_adminrig_1548jinnescurtisstanford/D_2008_10_15_15_12_26_FLX04070166_1548jinnescurtisstanford_FullAnalysis
Full Path: /data/2008_10_15/R_2008_10_15_16_11_02_FLX04070166_adminrig_1548jinnescurtisstanford/D_2008_10_15_15_12_26_FLX04070166_1548jinnescurtisstanford_FullAnalysis
Read Header Len: 32
Name Length: 14
# of Bases: 206
Clip Qual Left: 5
Clip Qual Right: 187
Clip Adap Left: 0
Clip Adap Right: 0
Flowgram: 1.04 0.00 1.01 0.00 0.00 1.00 0.00 1.00 0.00 1.05 0.00 0.91 0.10 1.07 0.95 1.01 0.00 0.06 0.93 0.02 0.03 1.06 1.18 0.09 1.00 0.05 0.90 0.11 0.07 1.99 0.11 0.02 1.96 1.04 0.13 0.01 2.83 0.10 1.97 0.06 0.11 1.04 0.13 0.03 0.98 1.15 0.07 1.00 0.07 0.08 0.98 0.11 1.92 0.05 0.04 2.96 1.02 1.02 0.04 0.93 1.00 0.13 0.04 1.00 1.03 0.08 0.97 0.13 0.11 1.88 0.09 0.05 1.02 1.89 0.07 0.11 0.98 0.05 0.07 1.01 0.08 0.05 1.01 0.13 1.00 0.07 0.10 1.04 0.10 0.04 0.98 0.12 1.03 0.96 0.11 0.07 1.00 0.09 0.03 1.03 0.11 1.95 1.06 0.13 0.05 1.00 0.13 0.11 1.00 0.09 0.03 2.89 0.08 0.95 0.09 1.03 1.02 1.05 1.07 0.08 0.12 2.81 0.08 0.08 1.00 1.07 0.07 0.05 1.86 0.12 0.98 0.06 2.00 0.11 1.02 0.11 0.08 1.88 0.13 1.03 0.13 0.98 0.15 0.11 1.03 1.03 1.04 0.18 0.98 0.13 0.15 1.04 0.11 1.01 0.13 0.06 1.01 0.06 1.02 0.08 0.99 0.14 0.99 0.09 0.05 1.09 0.04 0.07 2.96 0.09 2.03 0.13 2.96 1.13 0.08 1.03 0.07 0.99 0.11 0.05 1.05 1.04 0.09 0.07 1.00 1.03 0.09 0.06 1.06 1.04 2.94 0.18 0.06 0.93 0.10 1.10 0.11 2.02 0.17 1.00 1.03 0.06 0.11 0.96 0.04 3.00 0.11 0.07 1.99 0.10 2.03 0.12 0.97 0.16 0.01 2.09 0.14 1.04 0.16 0.06 1.03 0.14 1.12 0.12 0.05 0.96 1.01 0.10 0.14 0.94 0.03 0.12 1.10 0.92 0.09 1.10 1.04 1.02 0.12 0.97 2.00 0.15 1.08 0.04 1.03 1.04 0.03 0.09 5.16 1.02 0.09 0.13 2.66 0.09 0.05 1.06 0.07 0.89 0.05 0.12 1.10 0.16 0.06 1.01 0.13 1.00 0.14 0.98 0.09 2.92 1.28 0.03 2.95 0.98 0.16 0.08 0.95 0.96 1.09 0.08 1.07 1.01 0.16 0.06 4.52 0.12 1.03 0.07 0.09 1.03 0.14 0.03 1.01 1.99 1.05 0.14 1.03 0.13 0.03 1.10 0.10 0.96 0.11 0.99 0.12 0.05 0.94 2.83 0.14 0.12 0.96 0.00 1.00 0.11 0.14 1.98 0.08 0.11 1.04 0.01 0.11 2.03 0.15 2.05 0.10 0.03 0.93 0.01 0.08 0.12 0.00 0.16 0.05 0.07 0.08 0.11 0.07 0.05 0.04 0.10 0.05 0.05 0.03 0.07 0.03 0.04 0.04 0.06 0.03 0.05 0.04 0.09 0.03 0.08 0.03 0.07 0.02 0.05 0.02 0.06 0.01 0.05 0.04 0.06 0.02 0.04 0.04 0.04 0.03 0.03 0.06 0.06 0.03 0.02 0.02 0.08 0.03 0.01 0.01 0.06 0.03 0.01 0.03 0.04 0.02 0.00 0.02 0.05 0.00 0.02 0.02 0.03 0.00 0.02 0.02 0.04 0.01 0.00 0.01 0.05
Flow Indexes: 1 3 6 8 10 12 14 15 16 19 22 23 25 27 30 30 33 33 34 37 37 37 39 39 42 45 46 48 51 53 53 56 56 56 57 58 60 61 64 65 67 70 70 73 74 74 77 80 83 85 88 91 93 94 97 100 102 102 103 106 109 112 112 112 114 116 117 118 119 122 122 122 125 126 129 129 131 133 133 135 138 138 140 142 145 146 147 149 152 154 157 159 161 163 166 169 169 169 171 171 173 173 173 174 176 178 181 182 185 186 189 190 191 191 191 194 196 198 198 200 201 204 206 206 206 209 209 211 211 213 216 216 218 221 223 226 227 230 233 234 236 237 238 240 241 241 243 245 246 249 249 249 249 249 250 253 253 253 256 258 261 264 266 268 270 270 270 271 273 273 273 274 277 278 279 281 282 285 285 285 285 285 287 290 293 294 294 295 297 300 302 304 307 308 308 308 311 313 316 316 319 322 322 324 324 327
Bases: tcagAGACGCACTCAATTATTTCCATAGCTTGGGTAGTGTCAATAATGCTGCTATGAACATGGGAGTACAAATATTCTTCAAGATACTGATCTCATTTCCTTTAGATATATACCCAGAAGTGAAATTCCTGGATCACATAGTAGTTCTATTTTTATTTGATGAGAAACTTTATACTATTTTTCATAActgagcgggctggcaaggc
Quality Scores: 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 34 34 34 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 36 36 36 36 36 38 25 25 25 38 37 37 37 37 37 37 33 33 34 37 37 37 37 37 37 37 38 34 20 20 26 26 20 34 38 37 37 37 37 37 37 37 37 37 38 38 38 37 37 37 37 37 37 37 37 37 37
""".split('\n')
def test_get_header_info(self):
"""get_header_info should return a sff file common header as a dict"""
header = get_header_info(self.rec)
self.assertEqual(len(header), 11)
self.assertEqual(header['Key Length'], '4')
self.assertEqual(header['Key Sequence'], 'TCAG')
def test_get_summaries(self):
"""get_summaries should return a generator of the summaries"""
summaries = get_summaries(self.rec,number_list = [1])
sum_list = list(summaries)
self.assertEqual(len(sum_list), 1)
self.assertEqual(isinstance(summaries, GeneratorType), True)
self.assertEqual(len(sum_list[0]), 18)
self.assertEqual(sum_list[0][0], '>FIQU8OX05F8ILF')
summaries = get_summaries(self.rec,name_list = ['FIQU8OX05GCVRO'])
sum_list = list(summaries)
self.assertEqual(len(sum_list), 1)
self.assertEqual(isinstance(summaries, GeneratorType), True)
self.assertEqual(len(sum_list[0]), 18)
self.assertEqual(sum_list[0][0], '>FIQU8OX05GCVRO')
summaries = get_summaries(self.rec,all_sums = True )
sum_list = list(summaries)
self.assertEqual(len(sum_list), 2)
self.assertEqual(isinstance(summaries, GeneratorType), True)
self.assertEqual(len(sum_list[0]), 18)
self.assertEqual(sum_list[0][0], '>FIQU8OX05GCVRO')
self.assertEqual(sum_list[1][0], '>FIQU8OX05F8ILF')
summaries = get_summaries(self.rec,number_list = [0],
name_list =['FIQU8OX05GCVRO'])
self.assertRaises(AssertionError,list,summaries)
summaries = get_summaries(self.rec)
self.assertRaises(ValueError,list, summaries)
def test_get_all_summaries(self):
"""get_all_summaries should return a list of the summaries"""
summaries = get_all_summaries(self.rec)
self.assertEqual(len(summaries), 2)
self.assertEqual(isinstance(summaries,list), True)
self.assertEqual(len(summaries[0]), 18)
self.assertEqual(summaries[0][0], '>FIQU8OX05GCVRO')
self.assertEqual(summaries[1][0], '>FIQU8OX05F8ILF')
def test_split_summary(self):
"""split_summary should return the info of a flowgram header."""
summaries = get_all_summaries(self.rec)
sum_dict = split_summary(summaries[0])
self.assertEqual(len(sum_dict), 18)
self.assertEqual(sum_dict['Name'], 'FIQU8OX05GCVRO')
assert 'Flowgram' in sum_dict
assert 'Bases' in sum_dict
sum_dict = split_summary(summaries[1])
self.assertEqual(len(sum_dict), 18)
self.assertEqual(sum_dict['Name'], 'FIQU8OX05F8ILF')
assert 'Flowgram' in sum_dict
assert 'Bases' in sum_dict
def test_parse_sff(self):
"""SFParser should read in the SFF file correctly."""
flows, head = parse_sff(self.rec)
self.assertEqual(len(flows),2)
self.assertEqual(len(head), 11)
self.assertEqual(head['Key Length'], '4')
self.assertEqual(head['Key Sequence'], 'TCAG')
self.assertEqual(flows[0].Name, 'FIQU8OX05GCVRO')
self.assertEqual(flows[1].Name, 'FIQU8OX05F8ILF')
def test_lazy_parse_sff_handle(self):
"""LazySFParser should read in the SFF file correctly."""
flows, head = lazy_parse_sff_handle(self.rec)
flows = list(flows)
self.assertEqual(len(flows),2)
self.assertEqual(len(head), 11)
self.assertEqual(head['Key Length'], '4')
self.assertEqual(head['Key Sequence'], 'TCAG')
self.assertEqual(flows[0].Name, 'FIQU8OX05GCVRO')
self.assertEqual(flows[1].Name, 'FIQU8OX05F8ILF')
if __name__ == "__main__":
main()
|
