help=
'A range for sampling kmer by kmer number, use "[]" to include margin, and "()" to exclude margin.'
)
args = parser.parse_args()
# args = parser.parse_args(['-i', 'kmer.json', '-o', 'kmer.sample.json', '-r', '[2300, 10000]'])
inputFile = args.input
outputFile = args.output
rang = args.range
print('Sampling range is {0}'.format(rang))
left = int(rang[1:-1].split(',')[0])
right = int(rang[1:-1].split(',')[1])
if rang[0] == '[':
left -= 1
else:
pass
if rang[-1] == ']':
right += 1
else:
pass
count = 0
countPass = 0
beads = seqIO.beadJson(inputFile)
with open(outputFile, 'w') as f:
for item in beads:
count += 1
kmerNumber = len(list(item.values())[0])
if kmerNumber > left and kmerNumber < right:
countPass += 1
f.write('{0}\n'.format(json.dumps(item)))
print(count, countPass)
from metaSeq import io as seqIO
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input', help='Input Kmer json file.')
parser.add_argument('-o', '--output', help='Output pairwise jacarrd.')
args = parser.parse_args()
#args = parser.parse_args(['-i', 'kmer.sample.json', '-o', 'kmer.sample.nrdt.json'])
inputFile = args.input
outputFile = args.output
with open('kmer.sample.nrdt.json', 'r') as f:
nrd = json.load(f)
#% Test the pairwise distance
from itertools import combinations
beadPool = []
for item in seqIO.beadJson(inputFile):
barcode = list(item.keys())[0]
kmers = item[barcode]
beadPool.append((barcode, kmers))
pd = []
count = 0
for pair in combinations(beadPool, 2):
count += 1
if len(pair[0]) < len(pair[1]):
k1 = pair[0]
k2 = pair[1]
else:
k1 = pair[1]
k2 = pair[0]
share = 0
import argparse
from metaSeq import kmer
from metaSeq import io as seqIO
from itertools import combinations
import random
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input', help='JSON kmer file.')
parser.add_argument('-o', '--output', help='Output file.')
args = parser.parse_args()
# args = parser.parse_args(['-i', 'kmer.sample.json', '-o', 'kmer.distance.tsv'])
inputFile = args.input
outputFile = args.output
print('Read in kmer json file')
kmerParser = seqIO.beadJson('kmer.sample.json')
kmers = []
for item in kmerParser:
currentBead = list(list(item.items())[0])
currentBead[1] = random.sample(currentBead[1], len(currentBead[1]) // 10)
kmers.append(currentBead)
print('Found {0} beads'.format(len(kmers)))
print('Start calculating kmer distance')
mashD = []
count = 0
for pairs in combinations(kmers, 2):
count += 1
if count // 100000 > 0 and count % 10000 == 0:
print(count)
k1 = pairs[0]
k2 = pairs[1]
if item[2] > 0.02:
f.write('{0}\t{1}\t{2}\n'.format(item[0], item[1], item[2]))
'''
#%%
''' Extract bead sequences by module number '''
from metaSeq import io as seqIO
from metaSeq import bead
module = {}
with open('kmer.jcd.0.02.module.txt', 'r') as f:
f.readline()
for line in f:
line = line.strip('\n').split('\t')
module[line[0]] = line[1]
print(len(module))
cluster = {}
for item in list(set(module.values())):
cluster[item] = []
print(len(cluster))
beads = seqIO.beadJson('CL100077200_L01.json')
for item in beads:
b = bead.beadSequence(item)
classNumber = module.get(b.barcode, False)
if classNumber:
cluster[classNumber] += b.fastaSequences()
print(len(cluster))
for key, value in cluster.items():
seqIO.write_seqs(value, 'cluster/{0}.fa'.format(key), fastx='a', mode='w')