import numpy as np
from pbcore.io import CmpH5Reader
from GenomicConsensus import reference
from projutils import getReads
from bqcy.bqcy import run_bqcy
cmpH5 = CmpH5Reader(
'/home/nick/workspace/btry6790_project/PXO99A_ref_wo_one_copy_212kb_repeat.cmp.h5'
)
reference.loadFromFile(
"/home/nick/workspace/btry6790_project/ref_PXO99A_genome_reference_wo_one_copy_212k_repeat/sequence/ref_PXO99A_genome_reference_wo_one_copy_212k_repeat.fasta",
cmpH5)
tmplSeq, realTmplLen, readSeqs, qvInfo = getReads(cmpH5, reference,
(146000, 146050), 64, 100)
#print(readSeqs[:, 65:])
#exit()
print("POA Consensus: " + ''.join(map(chr, tmplSeq.tolist())))
tmplSeq = np.zeros((64), dtype=np.uint8)
tmplOrds = map(ord, "A" * 50)
tmplSeq[:len(tmplOrds)] = tmplOrds
results = np.zeros(8 * tmplSeq.shape[0], dtype=np.float64)
origTmplScore, bestMutantScore, bestMutatedSeq = run_bqcy(
tmplSeq, readSeqs, qvInfo, results)
print("Polished: " + ''.join(map(chr, np.asarray(bestMutatedSeq).tolist())))
print("Fake Template: " + ''.join(map(chr, np.asarray(tmplSeq).tolist())))
print(results)
import numpy as np from projutils import getReads tmplSeq, realTmplLen, readSeqs, qvInfo = getReads() #sanity_check(tmplSeq, realTmplLen, readSeqs, qvInfo) #[C2.AllQVsModel] # s stands for slope Match = 0.2627555 Mismatch = -1.09688872 MismatchS = -0.01637988 Branch = -0.60275947 BranchS = -0.02682689 DeletionN = -1.00012494 DeletionWithTag = 0.06000148 DeletionWithTagS = -0.02579358 Nce = -0.15864559 NceS = -0.04403654 Merge = -1.02398814 MergeS = -0.12135255 #metrics InsertionIdx = 0 MergeIdx = 1 DeletionIdx = 2 DeletionTagIdx = 3 SubstitutionIdx = 4 readLength = 256 tmplLength = 256
import numpy as np
from pbcore.io import CmpH5Reader
from GenomicConsensus import reference
from projutils import getReads
from bqcy.bqcy import getTemplateScore
from bqfast.bqfast import run_bqfast
cmpH5 = CmpH5Reader('/home/nick/workspace/btry6790_project/PXO99A_ref_wo_one_copy_212kb_repeat.cmp.h5')
reference.loadFromFile("/home/nick/workspace/btry6790_project/ref_PXO99A_genome_reference_wo_one_copy_212k_repeat/sequence/ref_PXO99A_genome_reference_wo_one_copy_212k_repeat.fasta", cmpH5)
#tmplSeq, realTmplLen, readSeqs, qvInfo = getReads(cmpH5, reference, (146000, 146100), 128, 100)
tmplSeq, realTmplLen, readSeqs, qvInfo = getReads(cmpH5, reference, (146000, 146050), 64, 100)
print("Real Template: " + ''.join(map(chr, tmplSeq.tolist())))
tmplSeq = np.zeros((64), dtype=np.uint8)
tmplOrds = map(ord, "A" * 50)
tmplSeq[:len(tmplOrds)] = tmplOrds
tmplScore = getTemplateScore(tmplSeq, readSeqs, qvInfo)
results, polishedTmplSeq = run_bqfast(tmplSeq, tmplSeq.shape[0], tmplScore, readSeqs, qvInfo)
print("Polished: " + ''.join(map(chr, polishedTmplSeq.tolist())))
print("Fake Template: " + ''.join(map(chr, tmplSeq.tolist())))
print(results[:tmplSeq.shape[0] * 8])
import numpy as np from projutils import getReads tmplSeq, realTmplLen, readSeqs, qvInfo = getReads() #sanity_check(tmplSeq, realTmplLen, readSeqs, qvInfo) #[C2.AllQVsModel] # s stands for slope Match = 0.2627555 Mismatch = -1.09688872 MismatchS = -0.01637988 Branch = -0.60275947 BranchS = -0.02682689 DeletionN = -1.00012494 DeletionWithTag = 0.06000148 DeletionWithTagS = -0.02579358 Nce = -0.15864559 NceS = -0.04403654 Merge = -1.02398814 MergeS = -0.12135255 #metrics InsertionIdx = 0 MergeIdx = 1 DeletionIdx = 2 DeletionTagIdx = 3 SubstitutionIdx = 4 readLength = 256 tmplLength = 256
from ConsensusCore import *
import numpy as np
from projutils import getReads, sanity_check
from pbcore.io import CmpH5Reader
from GenomicConsensus import reference
cmpH5 = CmpH5Reader('/home/nick/workspace/btry6790_project/PXO99A_ref_wo_one_copy_212kb_repeat.cmp.h5')
reference.loadFromFile("/home/nick/workspace/btry6790_project/ref_PXO99A_genome_reference_wo_one_copy_212k_repeat/sequence/ref_PXO99A_genome_reference_wo_one_copy_212k_repeat.fasta", cmpH5)
tmplSeq, realTmplLen, fwdSeqs, qvInfo = getReads(cmpH5, reference, (146000, 146050), 64, 100, real_quiver=True)
np.set_printoptions(linewidth=200)
totalScore = 0
for read in range(len(fwdSeqs)):
features = QvSequenceFeatures(fwdSeqs[read],
FloatFeature(qvInfo[0, :len(fwdSeqs[read]), read].astype(np.float32)),
FloatFeature(qvInfo[4, :len(fwdSeqs[read]), read].astype(np.float32)),
FloatFeature(qvInfo[2, :len(fwdSeqs[read]), read].astype(np.float32)),
FloatFeature(qvInfo[3, :len(fwdSeqs[read]), read].astype(np.float32)),
FloatFeature(qvInfo[1, :len(fwdSeqs[read]), read].astype(np.float32)))
params = QvModelParams(0.2627555,
-1.09688872,
-0.01637988,
-0.60275947,
-0.02682689,
-1.00012494,
0.06000148,
-0.02579358,
-0.15864559,
