def testErwiniaPhage(self):
"""
Test values corresponding to the following observed BLAST match against
Erwinia phage phiEaH2, complete genome.
<Iteration>
<Iteration_iter-num>3</Iteration_iter-num>
<Iteration_query-ID>Query_3</Iteration_query-ID>
<Iteration_query-def>SK7F6:834:2401</Iteration_query-def>
<Iteration_query-len>111</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|431810571|ref|NC_019929.1|</Hit_id>
<Hit_def>Erwinia phage phiEaH2, complete genome</Hit_def>
<Hit_accession>NC_019929</Hit_accession>
<Hit_len>243050</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>37.3537</Hsp_bit-score>
<Hsp_score>40</Hsp_score>
<Hsp_evalue>0.0813089</Hsp_evalue>
<Hsp_query-from>86</Hsp_query-from>
<Hsp_query-to>108</Hsp_query-to>
<Hsp_hit-from>33712</Hsp_hit-from>
<Hsp_hit-to>33690</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>-1</Hsp_hit-frame>
<Hsp_identity>22</Hsp_identity>
<Hsp_positive>22</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>23</Hsp_align-len>
<Hsp_qseq>GATAACTTCCAGGAATTCGTCCA</Hsp_qseq>
<Hsp_hseq>GATAACTTCCAGGAATTCGTTCA</Hsp_hseq>
<Hsp_midline>|||||||||||||||||||| ||</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>5660</Statistics_db-num>
<Statistics_db-len>168142520</Statistics_db-len>
<Statistics_hsp-len>26</Statistics_hsp-len>
<Statistics_eff-space>14279605600</Statistics_eff-space>
<Statistics_kappa>0.41</Statistics_kappa>
<Statistics_lambda>0.625</Statistics_lambda>
<Statistics_entropy>0.78</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
"""
self.assertAlmostEqual(0.0813089,
bitScoreToEValue(bitScore=37.3537,
dbSize=168142520,
dbSequenceCount=5660,
queryLength=111,
lengthAdjustment=26),
places=4)
def testErwiniaPhage(self):
"""
Test values corresponding to the following observed BLAST match against
Erwinia phage phiEaH2, complete genome.
<Iteration>
<Iteration_iter-num>3</Iteration_iter-num>
<Iteration_query-ID>Query_3</Iteration_query-ID>
<Iteration_query-def>SK7F6:834:2401</Iteration_query-def>
<Iteration_query-len>111</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|431810571|ref|NC_019929.1|</Hit_id>
<Hit_def>Erwinia phage phiEaH2, complete genome</Hit_def>
<Hit_accession>NC_019929</Hit_accession>
<Hit_len>243050</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>37.3537</Hsp_bit-score>
<Hsp_score>40</Hsp_score>
<Hsp_evalue>0.0813089</Hsp_evalue>
<Hsp_query-from>86</Hsp_query-from>
<Hsp_query-to>108</Hsp_query-to>
<Hsp_hit-from>33712</Hsp_hit-from>
<Hsp_hit-to>33690</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>-1</Hsp_hit-frame>
<Hsp_identity>22</Hsp_identity>
<Hsp_positive>22</Hsp_positive>
<Hsp_gaps>0</Hsp_gaps>
<Hsp_align-len>23</Hsp_align-len>
<Hsp_qseq>GATAACTTCCAGGAATTCGTCCA</Hsp_qseq>
<Hsp_hseq>GATAACTTCCAGGAATTCGTTCA</Hsp_hseq>
<Hsp_midline>|||||||||||||||||||| ||</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>5660</Statistics_db-num>
<Statistics_db-len>168142520</Statistics_db-len>
<Statistics_hsp-len>26</Statistics_hsp-len>
<Statistics_eff-space>14279605600</Statistics_eff-space>
<Statistics_kappa>0.41</Statistics_kappa>
<Statistics_lambda>0.625</Statistics_lambda>
<Statistics_entropy>0.78</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
"""
self.assertAlmostEqual(0.0813089,
bitScoreToEValue(bitScore=37.3537,
dbSize=168142520,
dbSequenceCount=5660,
queryLength=111,
lengthAdjustment=26),
places=4)
def testTrivial(self):
"""
For a bit score of 1.0 on a database of size 1 with a query length
1, and no length adjustment, we should get an e-value of 0.5
"""
self.assertEqual(0.5, bitScoreToEValue(bitScore=1.0,
dbSize=1,
dbSequenceCount=1,
queryLength=1,
lengthAdjustment=0))
def testTrivial(self):
"""
For a bit score of 1.0 on a database of size 1 with a query length
1, and no length adjustment, we should get an e-value of 0.5
"""
self.assertEqual(
0.5,
bitScoreToEValue(bitScore=1.0,
dbSize=1,
dbSequenceCount=1,
queryLength=1,
lengthAdjustment=0))
from dark.blast.score import bitScoreToEValue
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description='Convert a bit score to an e-value.')
parser.add_argument(
'--bitScore', type=float, required=True,
help='The bit score to convert')
parser.add_argument(
'--dbSize', type=int, required=True,
help='The total number of bases in the sequence database.')
parser.add_argument(
'--dbSequenceCount', type=int, required=True,
help='The number of sequences in the database.')
parser.add_argument(
'--queryLength', type=int, required=True,
help='The length of the query sequence.')
parser.add_argument(
'--lengthAdjustment', type=int, required=True,
help='The length adjustment.')
args = parser.parse_args()
print(bitScoreToEValue(args.bitScore, args.dbSize, args.dbSequenceCount,
args.queryLength, args.lengthAdjustment))
def testParameciumBursaria(self):
"""
Test values corresponding to the following observed BLAST match against
Paramecium bursaria Chlorella virus NE-JV-1, partial genome.
(Long lines are continued with a \ to keep PEP-8 quiet.)
<Iteration>
<Iteration_iter-num>14</Iteration_iter-num>
<Iteration_query-ID>Query_14</Iteration_query-ID>
<Iteration_query-def>SK7F6:99:509</Iteration_query-def>
<Iteration_query-len>172</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|448932590|gb|JX997176.1|</Hit_id>
<Hit_def>Paramecium bursaria Chlorella virus NE-JV-1, partial \
genome</Hit_def>
<Hit_accession>JX997176</Hit_accession>
<Hit_len>326559</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>42.7638</Hsp_bit-score>
<Hsp_score>46</Hsp_score>
<Hsp_evalue>0.0359052</Hsp_evalue>
<Hsp_query-from>93</Hsp_query-from>
<Hsp_query-to>164</Hsp_query-to>
<Hsp_hit-from>140106</Hsp_hit-from>
<Hsp_hit-to>140038</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>-1</Hsp_hit-frame>
<Hsp_identity>55</Hsp_identity>
<Hsp_positive>55</Hsp_positive>
<Hsp_gaps>3</Hsp_gaps>
<Hsp_align-len>72</Hsp_align-len>
<Hsp_qseq>AGGAATCCCTAAATGAAGTCCAAGAAGAAATCCCCTGAAGGAATTATAAAGAGA\
AATCCCTGAAGTAATTCC</Hsp_qseq>
<Hsp_hseq>AGAAATCCCTGAA-GAAATCCCTGAAGACATCCC-TGAAGAAATCCCTGA-AGA\
AATCCCTGAAGAAATCCC</Hsp_hseq>
<Hsp_midline>|| ||||||| || ||| ||| ||||| ||||| ||||| ||| | \
|||||||||||||| ||| ||</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>1456080</Statistics_db-num>
<Statistics_db-len>1931895878</Statistics_db-len>
<Statistics_hsp-len>30</Statistics_hsp-len>
<Statistics_eff-space>268126313876</Statistics_eff-space>
<Statistics_kappa>0.41</Statistics_kappa>
<Statistics_lambda>0.625</Statistics_lambda>
<Statistics_entropy>0.78</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
"""
self.assertAlmostEqual(0.0359052,
bitScoreToEValue(bitScore=42.7638,
dbSize=1931895878,
dbSequenceCount=1456080,
queryLength=172,
lengthAdjustment=30),
places=4)
def testParameciumBursaria(self):
"""
Test values corresponding to the following observed BLAST match against
Paramecium bursaria Chlorella virus NE-JV-1, partial genome.
(Long lines are continued with a \ to keep PEP-8 quiet.)
<Iteration>
<Iteration_iter-num>14</Iteration_iter-num>
<Iteration_query-ID>Query_14</Iteration_query-ID>
<Iteration_query-def>SK7F6:99:509</Iteration_query-def>
<Iteration_query-len>172</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|448932590|gb|JX997176.1|</Hit_id>
<Hit_def>Paramecium bursaria Chlorella virus NE-JV-1, partial \
genome</Hit_def>
<Hit_accession>JX997176</Hit_accession>
<Hit_len>326559</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>42.7638</Hsp_bit-score>
<Hsp_score>46</Hsp_score>
<Hsp_evalue>0.0359052</Hsp_evalue>
<Hsp_query-from>93</Hsp_query-from>
<Hsp_query-to>164</Hsp_query-to>
<Hsp_hit-from>140106</Hsp_hit-from>
<Hsp_hit-to>140038</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>-1</Hsp_hit-frame>
<Hsp_identity>55</Hsp_identity>
<Hsp_positive>55</Hsp_positive>
<Hsp_gaps>3</Hsp_gaps>
<Hsp_align-len>72</Hsp_align-len>
<Hsp_qseq>AGGAATCCCTAAATGAAGTCCAAGAAGAAATCCCCTGAAGGAATTATAAAGAGA\
AATCCCTGAAGTAATTCC</Hsp_qseq>
<Hsp_hseq>AGAAATCCCTGAA-GAAATCCCTGAAGACATCCC-TGAAGAAATCCCTGA-AGA\
AATCCCTGAAGAAATCCC</Hsp_hseq>
<Hsp_midline>|| ||||||| || ||| ||| ||||| ||||| ||||| ||| | \
|||||||||||||| ||| ||</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>1456080</Statistics_db-num>
<Statistics_db-len>1931895878</Statistics_db-len>
<Statistics_hsp-len>30</Statistics_hsp-len>
<Statistics_eff-space>268126313876</Statistics_eff-space>
<Statistics_kappa>0.41</Statistics_kappa>
<Statistics_lambda>0.625</Statistics_lambda>
<Statistics_entropy>0.78</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
"""
self.assertAlmostEqual(0.0359052,
bitScoreToEValue(bitScore=42.7638,
dbSize=1931895878,
dbSequenceCount=1456080,
queryLength=172,
lengthAdjustment=30),
places=4)