/usr/lib/python2.7/dist-packages/pbsuite/utils/mapStats.py is in python-pbsuite-utils 15.8.24+dfsg-2.
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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 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 | #!/usr/bin/python
"""
Parse a directory of m4 files and report mapping stats like:
Number of Reads
Number of Subreads
Mean Subread Length
Mean Alignment Length
Mean #Hits per Read
Mean Accuracy
Mean Score
"""
import sys, os, glob
from collections import defaultdict
from pbsuite.utils.FileHandlers import M4File
from pbsuite.utils.summarizeAssembly import *
def collectStats(stats, input):
if input.endswith(".m4"):
parser = M4File(input)
elif input.endswith(".m5"):
parser = M5File(input)
reads = defaultdict(list)
subreads = defaultdict(list)
nSubs = 0
numBases = 0
numAlignedBases = 0
tailLengths = []
for line in parser:
name = line.qname.split('/')[1]
reads[name].append(line)
subreads[line.qname].append(line)
reads = dict(reads)
subreads = dict(subreads)
for read in reads:
readLength = {}
alignedLength = 0
for subr in reads[read]:
readLength[subr.qname] = subr.qseqlength
alignedLength += subr.qend - subr.qstart
stats["read"].append(sum(readLength.values()))
stats["aln_read"].append(alignedLength)
for sub in subreads.keys():
readLength = subreads[sub][0].qseqlength
stats["subread"].append(readLength)
alignedBases = 0
pieHits = []
for hit in subreads[sub]:
alnLength = hit.qend - hit.qstart
alignedBases += alnLength
pieHits.append(alnLength)
stats["hit"].append(alnLength)
stats["hitsim"].append(hit.pctsimilarity)
stats["aln_subread"].append(alignedBases)
if len(subreads[sub]) > 1:
stats["tail"].append(readLength)
stats["aln_tail"].extend(pieHits)
stats["unmappedTail"] += readLength - alignedBases
if __name__ == '__main__':
if len(sys.argv) != 2:
sys.stderr.write("Error! Invalid Number of Arguments\nMapStats.py <mappingDir | input.m4>\n Generates stats for every m4 alignemnt file in an inputDir or for a single m4 file\n")
sys.exit(1)
inputDir = sys.argv[1]
stats = {"read": [],
"aln_read": [],
"subread": [],
"aln_subread":[],
"hit": [],
"hitsim": [],
"tail": [],
"aln_tail": [],
"unmappedTail": 0}
if os.path.isfile(inputDir):
if not inputDir.endswith('.m4'):
sys.stderr.write("Error! Specified file is not .m4!")
exit(1)
collectStats(stats,inputDir)
else:
a = glob.glob(os.path.join(inputDir, "*.m4"))
a.extend(glob.glob(os.path.join(inputDir, "*.m5")))
for input in a:
collectStats(stats, input)
print "Read Stats:"
read = getStats(stats["read"])
alnread = getStats(stats["aln_read"])
print "Number of Reads\t", read["numSeqs"]
print "Number of Bases\t", read["totalLength"]
print "Mean Read Length\t", read["mean"]
print "N50 Read Length\t", read["n50"]
print "Number of Aligned Bases\t", alnread["totalLength"]
print "Mean Aligned Read Length\t", alnread["mean"]
print "N50 Aligned Read Length\t", alnread["n50"]
print "Unmapped Bases\t", stats["unmappedTail"]
print
print "Subread Stats:"
subread = getStats(stats["subread"])
alnsubread = getStats(stats["aln_subread"])
print "Number of Subreads\t", subread["numSeqs"]
print "Total Subread Bases\t", subread["totalLength"]
print "Mean Subread Length\t", subread["mean"]
print "N50 Subread Length\t", subread["n50"]
print "Total Subread Aligned Bases\t", alnsubread["totalLength"]
print "Mean Subread Aligned Length\t", alnsubread["mean"]
print "N50 Subread Aligned Length\t", alnsubread["n50"]
print
print "Alignment Hit Stats:"
hit = getStats(stats["hit"])
hitsim = getStats(stats["hitsim"])
print "Number of Alignments\t", hit["numSeqs"]
print "Total Hit Aligned Bases\t", hit["totalLength"]
print "Mean Hit Aligned Length\t", hit["mean"]
print "N50 Hit Aligned Length\t", hit["n50"]
print "Mean Hit Percent Similarity\t", hitsim["mean"]
print
print "Tailed (Split) Hits Stats:"
tailhit = getStats(stats["tail"])
alntail = getStats(stats["aln_tail"])
print "Number of Tailed Reads\t", tailhit["numSeqs"]
print "Number of Tailed Bases\t", tailhit["totalLength"]
print "Mean Tailed Read Length\t", tailhit["mean"]
print "N50 Tailed Read Length\t", tailhit["n50"]
print "Total Tailed Aligned Bases\t", alntail["totalLength"]
print "Mean Tailed Alignment Length\t", alntail["mean"]
print "N50 Tailed Alignment Length\t", alntail["n50"]
print
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