a, t, i, d, s = counter(query, refer)
sc = 0
if align.cigar[0][1] == 4:
sc += align.cigar[0][0]
if align.cigar[-1][1] == 4:
sc += align.cigar[0][0]
accuracy += a
tot += t
insertions += i
deletions += d
subs += s
soft += sc
errCnt = float(insertions + deletions + subs)
stats = getStats(readLengths)
space = str(max([len(str(x)) for x in stats.values()]) + 2)
report = ("#Seqs | {numSeqs:%d,}\n"
"Min | {min:%d,}\n"
"1st Qu.| {FstQu:%d,}\n" + \
"Median | {median:%d,}\n" + \
"Mean | {mean:%d,}\n" + \
"3rd Qu.| {TrdQu:%d,}\n" + \
"Max | {max:%d,}\n" + \
"Total | {totalLength:%d,}\n" + \
"n50 | {n50:%d,}\n" + \
"n90 | {n90:%d,}\n" + \
"n95 | {n95:%d,}\n").replace("%d", str(space))
#print stats
print "Read Stats" #, json.dumps(getStats(readLengths), indent=4)
#!/usr/bin/python
import argparse, json
from pbsuite.jelly.Jelly import JellyProtocol
from pbsuite.utils.FileHandlers import FastaFile, FastqFile
from pbsuite.utils.summarizeAssembly import getStats
USAGE = """Get statistics on fasta/fastq sequences recorded in a Protocol.xml"""
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=USAGE, \
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("xml", metavar="XML", type=str, \
help="Protocol.xml with inputs listed")
args = parser.parse_args()
protocol = JellyProtocol(args.xml)
seqLengths = []
for i in protocol.inputs:
if i.endswith(".fasta"):
f = FastaFile(i)
for j in f.values():
seqLengths.append(len(j))
if i.endswith(".fastq"):
f = FastqFile(i)
for j in f.values():
seqLengths.append(len(j.seq))
print "Read Stats", json.dumps(getStats(seqLengths), indent=4)
#!/usr/bin/env python
import argparse, json
from pbsuite.jelly.Jelly import JellyProtocol
from pbsuite.utils.FileHandlers import FastaFile, FastqFile
from pbsuite.utils.summarizeAssembly import getStats
USAGE = """Get statistics on fasta/fastq sequences recorded in a Protocol.xml"""
if __name__ == '__main__':
parser = argparse.ArgumentParser(description=USAGE, \
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("xml", metavar="XML", type=str, \
help="Protocol.xml with inputs listed")
args = parser.parse_args()
protocol = JellyProtocol(args.xml)
seqLengths = []
for i in protocol.inputs:
if i.endswith(".fasta"):
f = FastaFile(i)
for j in f.values():
seqLengths.append(len(j))
if i.endswith(".fastq"):
f = FastqFile(i)
for j in f.values():
seqLengths.append(len(j.seq))
print "Read Stats", json.dumps(getStats(seqLengths), indent=4)