def main(useReadName, verbose):
a = shasta.Assembler()
print("Accessing data ...")
a.accessMarkers()
a.accessAlignmentCandidates()
if verbose:
a.accessAlignmentData()
a.accessReadGraph()
print("Writing to AlignmentCandidates.csv ...")
a.writeAlignmentCandidates(useReadName, verbose)
print("Done")
import argparse
import shasta
# Get the arguments.
parser = argparse.ArgumentParser(
description="Compute the phasing similarity between two oriented reads.")
parser.add_argument("readId0",
type=int,
help="The read id of the first oriented read.")
parser.add_argument("strand0",
type=int,
help="The strand (0 or 1) of the first oriented read.")
parser.add_argument("readId1",
type=int,
help="The read id of the second oriented read.")
parser.add_argument("strand1",
type=int,
help="The strand (0 or 1) of the second oriented read.")
arguments = parser.parse_args()
# Create the Assembler.
a = shasta.Assembler()
# Access what we need.
a.accessPhasingData()
# Do the work.
print(
a.computePhasingSimilarity(arguments.readId0, arguments.strand0,
arguments.readId1, arguments.strand1))
#!/usr/bin/python3
import os
import shasta
# Find the path to the docs directory.
thisScriptPath = os.path.realpath(__file__)
thisScriptDirectory = os.path.dirname(thisScriptPath)
thisScriptParentDirectory = os.path.dirname(thisScriptDirectory)
docsDirectory = thisScriptParentDirectory + '/docs'
# Initialize the assembler and access what we need.
a = shasta.Assembler(
smallDataFileNamePrefix='dataOnDisk/',
largeDataFileNamePrefix='DataOnDisk/')
a.accessReadsReadOnly()
a.accessReadNamesReadOnly()
a.accessKmers()
a.accessMarkers()
a.accessOverlaps()
a.accessAlignmentData()
a.accessMarkerGraphVertices()
a.setupConsensusCaller('SimpleConsensusCaller')
a.setDocsDirectory(docsDirectory)
a.explore()
#!/usr/bin/python3
import os
import shasta
import GetConfig
# Find the path to the docs directory.
thisScriptPath = os.path.realpath(__file__)
thisScriptDirectory = os.path.dirname(thisScriptPath)
thisScriptParentDirectory = os.path.dirname(thisScriptDirectory)
docsDirectory = thisScriptParentDirectory + '/docs'
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler.
a = shasta.Assembler(
largeDataFileNamePrefix='DataOnDisk/')
a.accessAllSoft()
a.setupConsensusCaller(config['Assembly']['consensusCaller'])
a.setDocsDirectory(docsDirectory)
a.explore()
import shasta
import GetConfig
import os
import sys
# Check that we have what we need.
if not os.path.lexists('data'):
raise Exception('Missing: data. Use SetupRunDirectory.py to set up the run directory.')
if not os.path.lexists('Data'):
raise Exception('Missing: Data. Use SetupRunDirectory.py to set up the run directory.')
if not os.path.lexists('threadLogs'):
raise Exception('Missing: threadLogs. Use SetupRunDirectory.py to set up the run directory.')
if not os.path.lexists('shasta.conf'):
raise Exception('Missing: configuration file shasta.conf. Sample available in shasta-install/conf.')
# Read the config file.
config = GetConfig.getConfig()
# Create the assembler.
useRunLengthReadsString = config['Reads']['useRunLengthReads']
if useRunLengthReadsString == 'True':
useRunLengthReads = True
elif useRunLengthReadsString == 'False':
useRunLengthReads = False
else:
raise RuntimeError("Configuration parameter useRunLengthReads in section Reads must be True or False.")
a = shasta.Assembler(useRunLengthReads = useRunLengthReads)
def initializeAssembler(config, fastaFileNames):
# Create the Assembler.
a = shasta.Assembler(createNew=True)
return a
#!/usr/bin/python3
import shasta
import GetConfig
import os
import sys
# Check that we have what we need.
if not os.path.lexists('Data'):
raise Exception(
'Missing: Data. Use SetupRunDirectory.py to set up the run directory.')
if not os.path.lexists('shasta.conf'):
raise Exception(
'Missing: configuration file shasta.conf. Sample available in shasta-install/conf.'
)
# Read the config file.
config = GetConfig.getConfig()
# Create the assembler.
a = shasta.Assembler(createNew=True)
