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from __future__ import print_function
import argparse
def main(args):
import pysam
import sys
printFP = args.printFalsePositives
alnFile = pysam.AlignmentFile(args.input, 'r')
totalNumReads = args.totalNumReads
currQueryName = ''
skipToNextAlignment = False
readsWithTrueAln = 0
readsSeen = 0
truePos = 0
falsePos = 0
falseNeg = 0
foundTrueAlignment = False
## True Neg are somewhat ill-defined in our context
prevRec = None
useNHTag = args.useNHTag
NHTagSum = 0
nhData = []
for rec in alnFile:
if rec.is_unmapped:
continue
qname = rec.qname[:-2]
# If this is a new read, remember the name
# and increment the counter
if qname != currQueryName:
readsSeen += 1
if useNHTag:
tagVal = rec.get_tag('NH')
NHTagSum += tagVal
nhData.append(tagVal)
if readsSeen % 1000000 == 0:
print("\r\rSaw {} reads --- thp = {:.2%}".format(readsSeen, \
float(truePos) / readsSeen), file=sys.stderr, end='')
currQueryName = qname
if not foundTrueAlignment:
falsePos += 1
if (printFP):
print(prevRec)
skipToNextAlignment = False
foundTrueAlignment = False
prevRec = rec
# If we already found the true hit
# for this read, don't bother processing
# this record
if not skipToNextAlignment:
# Process the record to find if its the true
# hit
currQueryName = qname
trueTxpName = qname.split(':')[2]
alignedTxpName = alnFile.getrname(rec.rname)
if (trueTxpName == alignedTxpName):
truePos += 1
skipToNextAlignment = True
foundTrueAlignment = True
falseNeg = totalNumReads - readsSeen
print('\n'.join(["Total Reads = {}" ,
"Reads Aligned = {}" ,
"True Pos = {}" ,
"False Pos = {}" ,
"False Neg = {}" ,
"Precision = {:.2%}",
"Recall = {:.2%}" ,
"TPH = {:.2%}",
"FDR = {:.2%}",
"F1 Score = {:.2%}"]).format(totalNumReads, readsSeen,
truePos, falsePos,
falseNeg, truePos / float(truePos + falsePos),
truePos / float(truePos + falseNeg),
truePos / float(readsSeen),
falsePos / float(falsePos + truePos),
(2*truePos) / float(2*truePos + falsePos + falseNeg)),
file=sys.stderr)
if useNHTag:
print("Average hits-per-read = {:.2}".format(
NHTagSum / float(totalNumReads)), file=sys.stderr)
if args.nhFreqFile:
import pickle
pickle.dump(nhData, args.nhFreqFile)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Compute statistics from synthetic SAM file.')
parser.add_argument('--input', type=str)
parser.add_argument('--totalNumReads', type=int)
parser.add_argument('--useNHTag', action='store_true')
parser.add_argument('--nhFreqFile', nargs='?', type=argparse.FileType('w'))
parser.add_argument('--printFalsePositives', action='store_true')
args = parser.parse_args()
main(args)
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