1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
#!/usr/bin/python3
import shasta
import GetConfig
import sys
helpMessage="""
This uses the LowHash method to find alignment candidates.
Invoke without arguments.
"""
# Check that there are no arguments.
if not len(sys.argv)==1:
print(helpMessage)
exit(1)
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessKmers()
a.accessMarkers()
# Do the computation.
a.findAlignmentCandidatesLowHash0(
m = int(config['MinHash']['m']),
hashFraction = float(config['MinHash']['hashFraction']),
minHashIterationCount = int(config['MinHash']['minHashIterationCount']),
alignmentCandidatesPerRead = float(config['MinHash']['alignmentCandidatesPerRead']),
minBucketSize = int(config['MinHash']['minBucketSize']),
maxBucketSize = int(config['MinHash']['maxBucketSize']),
minFrequency = int(config['MinHash']['minFrequency']))
|
