Make cleaning
This commit is contained in:
Eric Coissac
@@ -0,0 +1,604 @@
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#!/usr/bin/env python3
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import re
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import gzip
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import struct
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import sys
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import time
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import getopt
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from functools import cmp_to_key
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_dbenable=False
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#####
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#
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#
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# Generic file function
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#
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#
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#####
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def universalOpen(file):
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if isinstance(file,str):
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if file[-3:] == '.gz':
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rep = gzip.open(file)
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else:
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rep = open(file)
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else:
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rep = file
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return rep
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def universalTell(file):
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if isinstance(file, gzip.GzipFile):
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file=file.myfileobj
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return file.tell()
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def fileSize(file):
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if isinstance(file, gzip.GzipFile):
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file=file.myfileobj
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pos = file.tell()
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file.seek(0,2)
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length = file.tell()
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file.seek(pos,0)
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return length
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def progressBar(pos,max,reset=False,delta=[]):
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if reset:
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del delta[:]
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if not delta:
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delta.append(time.time())
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delta.append(time.time())
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delta[1]=time.time()
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elapsed = delta[1]-delta[0]
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percent = float(pos)/max * 100
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remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
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bar = '#' * int(percent/2)
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bar+= '|/-\\-'[pos % 5]
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bar+= ' ' * (50 - int(percent/2))
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sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
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#####
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#
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#
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# NCBI Dump Taxonomy reader
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#
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#
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#####
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def endLessIterator(endedlist):
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for x in endedlist:
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yield x
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while(1):
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yield endedlist[-1]
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class ColumnFile(object):
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def __init__(self,stream,sep=None,strip=True,types=None):
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if isinstance(stream,str):
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self._stream = open(stream)
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else:
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try:
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iter(stream)
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self._stream = stream
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except TypeError:
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raise ValueError('stream must be string or an iterator')
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self._delimiter=sep
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self._strip=strip
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if types:
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self._types=[x for x in types]
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for i in range(len(self._types)):
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if self._types[i] is bool:
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self._types[i]=ColumnFile.str2bool
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else:
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self._types=None
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def str2bool(x):
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return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
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str2bool = staticmethod(str2bool)
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def __iter__(self):
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return self
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def __next__(self):
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ligne = next(self._stream)
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data = ligne.split(self._delimiter)
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if self._strip or self._types:
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data = [x.strip() for x in data]
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if self._types:
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it = endLessIterator(self._types)
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data = [x[1](x[0]) for x in ((y,next(it)) for y in data)]
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return data
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def taxonCmp(t1,t2):
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if t1[0] < t2[0]:
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return -1
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elif t1[0] > t2[0]:
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return +1
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return 0
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def bsearchTaxon(taxonomy,taxid):
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taxCount = len(taxonomy)
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begin = 0
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end = taxCount
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oldcheck=taxCount
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check = int(begin + end / 2)
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while check != oldcheck and taxonomy[check][0]!=taxid :
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if taxonomy[check][0] < taxid:
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begin=check
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else:
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end=check
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oldcheck=check
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check = int((begin + end) / 2)
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if taxonomy[check][0]==taxid:
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return check
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else:
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return None
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def readNodeTable(file):
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file = universalOpen(file)
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nodes = ColumnFile(file,
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sep='|',
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types=(int,int,str,
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str,str,bool,
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int,bool,int,
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bool,bool,bool,str))
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print("Reading taxonomy dump file...", file=sys.stderr)
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taxonomy=[[n[0],n[2],n[1]] for n in nodes]
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print("List all taxonomy rank...", file=sys.stderr)
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ranks =list(set(x[1] for x in taxonomy))
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ranks.sort()
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ranks = {rank: index for index, rank in enumerate(ranks)}
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print("Sorting taxons...", file=sys.stderr)
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taxonomy.sort(key=lambda x: x[0])
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print("Indexing taxonomy...", file=sys.stderr)
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index = {}
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for t in taxonomy:
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index[t[0]]=bsearchTaxon(taxonomy, t[0])
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print("Indexing parent and rank...", file=sys.stderr)
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for t in taxonomy:
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t[1]=ranks[t[1]]
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t[2]=index[t[2]]
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return taxonomy,ranks,index
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def nameIterator(file):
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file = universalOpen(file)
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names = ColumnFile(file,
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sep='|',
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types=(int,str,
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str,str))
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for taxid,name,unique,classname,white in names:
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yield taxid,name,classname
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def mergedNodeIterator(file):
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file = universalOpen(file)
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merged = ColumnFile(file,
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sep='|',
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types=(int,int,str))
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for taxid,current,white in merged:
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yield taxid,current
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def deletedNodeIterator(file):
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file = universalOpen(file)
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deleted = ColumnFile(file,
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sep='|',
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types=(int,str))
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for taxid,white in deleted:
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yield taxid
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def readTaxonomyDump(taxdir):
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taxonomy,ranks,index = readNodeTable('%s/nodes.dmp' % taxdir)
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print("Adding scientific name...", file=sys.stderr)
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alternativeName=[]
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for taxid,name,classname in nameIterator('%s/names.dmp' % taxdir):
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alternativeName.append((name,classname,index[taxid]))
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if classname == 'scientific name':
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taxonomy[index[taxid]].append(name)
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print("Adding taxid alias...", file=sys.stderr)
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for taxid,current in mergedNodeIterator('%s/merged.dmp' % taxdir):
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index[taxid]=index[current]
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print("Adding deleted taxid...", file=sys.stderr)
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for taxid in deletedNodeIterator('%s/delnodes.dmp' % taxdir):
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index[taxid]=None
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return taxonomy,ranks,alternativeName,index
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#####
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#
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#
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# Genbank/EMBL sequence reader
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#
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#
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#####
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def entryIterator(file):
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file = universalOpen(file)
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rep =[]
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ligne = file.readline()
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while ligne:
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rep.append(ligne)
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if ligne == '//\n':
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rep = ''.join(rep)
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yield rep
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rep = []
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ligne = file.readline()
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def fastaEntryIterator(file):
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file = universalOpen(file)
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rep =[]
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ligne = file.readline()
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while ligne:
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if ligne[0] == '>' and rep:
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rep = ''.join(rep)
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yield rep
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rep = []
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rep.append(ligne)
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ligne = file.readline()
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if rep:
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rep = ''.join(rep)
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yield rep
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_cleanSeq = re.compile('[ \n0-9]+')
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def cleanSeq(seq):
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return _cleanSeq.sub('',seq)
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_gbParseID = re.compile('(?<=^LOCUS {7})[^ ]+(?= )',re.MULTILINE)
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_gbParseDE = re.compile('(?<=^DEFINITION {2}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
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_gbParseSQ = re.compile('(?<=^ORIGIN).+?(?=^//$)',re.MULTILINE+re.DOTALL)
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_gbParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
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def genbankEntryParser(entry):
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Id = _gbParseID.findall(entry)[0]
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De = ' '.join(_gbParseDE.findall(entry)[0].split())
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Sq = cleanSeq(_gbParseSQ.findall(entry)[0].upper())
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try:
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Tx = int(_gbParseTX.findall(entry)[0])
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except IndexError:
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Tx = None
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return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
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######################
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_cleanDef = re.compile('[\nDE]')
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def cleanDef(definition):
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return _cleanDef.sub('',definition)
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_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)
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_emblParseDE = re.compile('(?<=^DE {3}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
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_emblParseSQ = re.compile('(?<=^ ).+?(?=^//$)',re.MULTILINE+re.DOTALL)
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_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
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def emblEntryParser(entry):
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Id = _emblParseID.findall(entry)[0]
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De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
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Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
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try:
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Tx = int(_emblParseTX.findall(entry)[0])
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except IndexError:
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Tx = None
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return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
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######################
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_fastaSplit=re.compile(';\\W*')
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def parseFasta(seq):
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seq=seq.split('\n')
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title = seq[0].strip()[1:].split(None,1)
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id=title[0]
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if len(title) == 2:
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field = _fastaSplit.split(title[1])
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else:
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field=[]
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info = dict(x.split('=',1) for x in field if '=' in x)
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definition = ' '.join([x for x in field if '=' not in x])
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seq=(''.join([x.strip() for x in seq[1:]])).upper()
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return id,seq,definition,info
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def fastaEntryParser(entry):
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id,seq,definition,info = parseFasta(entry)
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Tx = info.get('taxid',None)
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if Tx is not None:
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match = re.search(r'taxon:(\d+)', Tx)
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if match:
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Tx = match.group(1)
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Tx=int(Tx)
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return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
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def sequenceIteratorFactory(entryParser,entryIterator):
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def sequenceIterator(file):
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for entry in entryIterator(file):
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yield entryParser(entry)
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return sequenceIterator
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def taxonomyInfo(entry,connection):
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taxid = entry['taxid']
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curseur = connection.cursor()
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curseur.execute("""
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select taxid,species,genus,family,
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taxonomy.scientificName(taxid) as sn,
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taxonomy.scientificName(species) as species_sn,
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taxonomy.scientificName(genus) as genus_sn,
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taxonomy.scientificName(family) as family_sn
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from
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(
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select alias as taxid,
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taxonomy.getSpecies(alias) as species,
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taxonomy.getGenus(alias) as genus,
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taxonomy.getFamily(alias) as family
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from taxonomy.aliases
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where id=%d ) as tax
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""" % taxid)
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rep = curseur.fetchone()
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entry['current_taxid']=rep[0]
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entry['species']=rep[1]
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entry['genus']=rep[2]
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entry['family']=rep[3]
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entry['scientific_name']=rep[4]
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entry['species_sn']=rep[5]
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entry['genus_sn']=rep[6]
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entry['family_sn']=rep[7]
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return entry
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#####
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#
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#
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# Binary writer
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#
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#
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#####
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def ecoSeqPacker(sq):
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compactseq = gzip.zlib.compress(bytes(sq['sequence'],"ascii"),9)
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cptseqlength = len(compactseq)
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delength = len(sq['definition'])
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totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
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packed = struct.pack('> I I 20s I I I %ds %ds' % (delength,cptseqlength),
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totalSize,
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sq['taxid'],
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bytes(sq['id'],"ascii"),
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delength,
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len(sq['sequence']),
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cptseqlength,
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bytes(sq['definition'],"ascii"),
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compactseq)
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assert len(packed) == totalSize+4, "error in sequence packing"
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return packed
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def ecoTaxPacker(tx):
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namelength = len(tx[3])
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totalSize = 4 + 4 + 4 + 4 + namelength
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packed = struct.pack('> I I I I I %ds' % namelength,
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totalSize,
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tx[0],
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tx[1],
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tx[2],
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namelength,
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bytes(tx[3],"ascii"))
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return packed
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def ecoRankPacker(rank):
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namelength = len(rank)
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packed = struct.pack('> I %ds' % namelength,
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namelength,
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bytes(rank, 'ascii'))
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return packed
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def ecoNamePacker(name):
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namelength = len(name[0])
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classlength= len(name[1])
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totalSize = namelength + classlength + 4 + 4 + 4 + 4
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packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
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totalSize,
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int(name[1]=='scientific name'),
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namelength,
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classlength,
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name[2],
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bytes(name[0], 'ascii'),
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bytes(name[1], 'ascii'))
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return packed
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def ecoSeqWriter(file,input,taxindex,parser):
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output = open(file,'wb')
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input = universalOpen(input)
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inputsize = fileSize(input)
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entries = parser(input)
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seqcount=0
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skipped = []
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output.write(struct.pack('> I',seqcount))
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progressBar(1, inputsize,reset=True)
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for entry in entries:
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if entry['taxid'] is not None:
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try:
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entry['taxid']=taxindex[entry['taxid']]
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except KeyError:
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entry['taxid']=None
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if entry['taxid'] is not None:
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seqcount+=1
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output.write(ecoSeqPacker(entry))
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else:
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skipped.append(entry['id'])
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where = universalTell(input)
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progressBar(where, inputsize)
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print(" Readed sequences : %d " % seqcount, end=' ', file=sys.stderr)
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else:
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skipped.append(entry['id'])
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print(file=sys.stderr)
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output.seek(0,0)
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output.write(struct.pack('> I',seqcount))
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output.close()
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return skipped
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||||
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def ecoTaxWriter(file,taxonomy):
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output = open(file,'wb')
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output.write(struct.pack('> I',len(taxonomy)))
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for tx in taxonomy:
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output.write(ecoTaxPacker(tx))
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output.close()
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def ecoRankWriter(file,ranks):
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output = open(file,'wb')
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output.write(struct.pack('> I',len(ranks)))
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rankNames = list(ranks.keys())
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rankNames.sort()
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for rank in rankNames:
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output.write(ecoRankPacker(rank))
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output.close()
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||||
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def nameCmp(n1,n2):
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name1=n1[0].upper()
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name2=n2[0].upper()
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||||
if name1 < name2:
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||||
return -1
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||||
elif name1 > name2:
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return 1
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return 0
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||||
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||||
|
||||
def ecoNameWriter(file,names):
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output = open(file,'wb')
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||||
output.write(struct.pack('> I',len(names)))
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||||
|
||||
names.sort(key=lambda x:x[0].upper())
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||||
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||||
for name in names:
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output.write(ecoNamePacker(name))
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||||
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||||
output.close()
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||||
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||||
def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
|
||||
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||||
ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
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ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
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||||
ecoNameWriter('%s.ndx' % prefix, taxonomy[2])
|
||||
|
||||
filecount = 0
|
||||
for filename in seqFileNames:
|
||||
filecount+=1
|
||||
sk=ecoSeqWriter('%s_%03d.sdx' % (prefix,filecount),
|
||||
filename,
|
||||
taxonomy[3],
|
||||
parser)
|
||||
if sk:
|
||||
print("Skipped entry :", file=sys.stderr)
|
||||
print(sk, file=sys.stderr)
|
||||
|
||||
def ecoParseOptions(arguments):
|
||||
opt = {
|
||||
'prefix' : 'ecodb',
|
||||
'taxdir' : 'taxdump',
|
||||
'parser' : sequenceIteratorFactory(genbankEntryParser,
|
||||
entryIterator)
|
||||
}
|
||||
|
||||
o,filenames = getopt.getopt(arguments,
|
||||
'ht:T:n:gfe',
|
||||
['help',
|
||||
'taxonomy=',
|
||||
'taxonomy_db=',
|
||||
'name=',
|
||||
'genbank',
|
||||
'fasta',
|
||||
'embl'])
|
||||
|
||||
for name,value in o:
|
||||
if name in ('-h','--help'):
|
||||
printHelp()
|
||||
exit()
|
||||
elif name in ('-t','--taxonomy'):
|
||||
opt['taxmod']='dump'
|
||||
opt['taxdir']=value
|
||||
elif name in ('-T','--taxonomy_db'):
|
||||
opt['taxmod']='db'
|
||||
opt['taxdb']=value
|
||||
elif name in ('-n','--name'):
|
||||
opt['prefix']=value
|
||||
elif name in ('-g','--genbank'):
|
||||
opt['parser']=sequenceIteratorFactory(genbankEntryParser,
|
||||
entryIterator)
|
||||
|
||||
elif name in ('-f','--fasta'):
|
||||
opt['parser']=sequenceIteratorFactory(fastaEntryParser,
|
||||
fastaEntryIterator)
|
||||
|
||||
elif name in ('-e','--embl'):
|
||||
opt['parser']=sequenceIteratorFactory(emblEntryParser,
|
||||
entryIterator)
|
||||
else:
|
||||
raise ValueError('Unknown option %s' % name)
|
||||
|
||||
return opt,filenames
|
||||
|
||||
def printHelp():
|
||||
print("-----------------------------------")
|
||||
print(" ecoPCRFormat.py")
|
||||
print("-----------------------------------")
|
||||
print("ecoPCRFormat.py [option] <argument>")
|
||||
print("-----------------------------------")
|
||||
print("-e --embl :[E]mbl format")
|
||||
print("-f --fasta :[F]asta format")
|
||||
print("-g --genbank :[G]enbank format")
|
||||
print("-h --help :[H]elp - print this help")
|
||||
print("-n --name :[N]ame of the new database created")
|
||||
print("-t --taxonomy :[T]axonomy - path to the taxonomy database")
|
||||
print(" :bcp-like dump from GenBank taxonomy database.")
|
||||
print("-----------------------------------")
|
||||
|
||||
if __name__ == '__main__':
|
||||
|
||||
opt,filenames = ecoParseOptions(sys.argv[1:])
|
||||
|
||||
taxonomy = readTaxonomyDump(opt['taxdir'])
|
||||
|
||||
ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
|
||||
|
||||
2606
jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
Normal file
2606
jupyterhub_volumes/web/obidoc/docs/cookbook/ecoprimers/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Designing new barcodes on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/ecoprimers/</link>
|
||||
<description>Recent content in Designing new barcodes on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/ecoprimers/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 168 KiB |
103
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
Normal file
103
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/Makefile
Normal file
@@ -0,0 +1,103 @@
|
||||
SHELL := /bin/bash
|
||||
FTPNCBI=ftp.ncbi.nlm.nih.gov
|
||||
GBURL=https://$(FTPNCBI)/genbank
|
||||
GBRELEASE_URL=$(GBURL)/GB_Release_Number
|
||||
|
||||
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
|
||||
|
||||
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
|
||||
|
||||
GBDIV_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E 'gb.+\.seq\.gz' \
|
||||
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
|
||||
| sort \
|
||||
| uniq)
|
||||
|
||||
GBDIV=bct inv mam phg pln pri rod vrl vrt
|
||||
DIRECTORIES=fasta fasta_fgs
|
||||
|
||||
GBFILE_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
|
||||
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
|
||||
|
||||
|
||||
SUFFIXES += .d
|
||||
NODEPS:=clean taxonomy
|
||||
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
|
||||
|
||||
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
|
||||
#Chances are, these files don't exist. GMake will create them and
|
||||
#clean up automatically afterwards
|
||||
-include $(DEPFILES)
|
||||
endif
|
||||
|
||||
|
||||
all: depends directories FORCE
|
||||
@make downloads
|
||||
|
||||
downloads: taxonomy fasta_files
|
||||
@echo Genbank Release number $(GBRELEASE)
|
||||
@echo all divisions : $(GBDIV_ALL)
|
||||
|
||||
FORCE:
|
||||
@sleep 1
|
||||
|
||||
.PHONY: all directories depends taxonomy fasta_files FORCE
|
||||
|
||||
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
|
||||
|
||||
division: $(GBDIV)
|
||||
|
||||
taxonomy: directories Release_$(GBRELEASE)/taxonomy
|
||||
|
||||
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
|
||||
|
||||
Release_$(GBRELEASE):
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
|
||||
@echo Create depends directory
|
||||
@mkdir -p Release_$(GBRELEASE)/depends
|
||||
@for f in ${GBFILE_ALL} ; do \
|
||||
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
|
||||
echo -e "\t@echo Downloading file : $$f..." ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
|
||||
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
|
||||
echo ; \
|
||||
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
|
||||
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_files="$$fasta_files $$fasta" ; \
|
||||
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
|
||||
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
|
||||
echo -e "\t@echo converting file : \$$< in fasta" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
|
||||
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
|
||||
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
|
||||
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
|
||||
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
|
||||
echo -e "\t || rm -f \$$@" ; \
|
||||
echo -e "\t@echo conversion of $$@ done." ; \
|
||||
echo ; \
|
||||
done > $@ ; \
|
||||
echo >> $@ ; \
|
||||
echo "fasta_files: $$fasta_files" >> $@ ;
|
||||
|
||||
Release_$(GBRELEASE)/taxonomy:
|
||||
mkdir -p $@
|
||||
curl -iL $(TAXOURL) \
|
||||
| tar -C $@ -zxf -
|
||||
2812
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
Normal file
2812
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Analysing an Illumina data set on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/illumina/</link>
|
||||
<description>Recent content in Analysing an Illumina data set on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/illumina/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 16 KiB |
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,26 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
|
||||
tttt
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,24 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
@@ -0,0 +1,329 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:56:19300:10949#0/1_sub[28..127] {"count":37,"merged_sample":{"29a_F260619":37},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":43}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:63:4595:15643#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagtactaccggcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:8807:7823#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtcataccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:19171:11413#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:8:6794:4925#0/1_sub[28..127]":"(t)->(g)@38"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaagtagtcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:44:5008:2115#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:53:16956:10563#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:54:10323:7022#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
||||
ttagccctaaacacaaataattatataaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:45:7460:13396#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatgcccgt
|
||||
>HELIUM_000100422_612GNAAXX:7:58:8409:9911#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:100:18844:15930#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaagcgcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:29:9723:20435#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:43:4660:16319#0/1_sub[28..126] {"count":22,"merged_sample":{"26a_F040644":22},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":42}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:103:11045:3860#0/1_sub[28..127] {"count":4,"merged_sample":{"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaagggcttggcggtgctttatgccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:67:10944:19430#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgtcagagtactaccggcaat
|
||||
agcttaaaactcaaaggacgtggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:56:6962:17278#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":7}}
|
||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:60:13553:20530#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
atgttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:35:13167:18371#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccggagaactactaggaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:105:1895:7593#0/1_sub[28..127] {"count":11,"merged_sample":{"29a_F260619":11},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":13}}
|
||||
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
||||
agcttaaaactcaaaggacctggcggtgcttcatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:118:15661:12736#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattatccgcaagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:30:8391:13152#0/1_sub[28..127] {"count":17,"merged_sample":{"13a_F730603":17},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":25}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:95:14375:10838#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":5}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:82:13334:18499#0/1_sub[28..127] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":10}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:11272:1128#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:6016:14767#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacgtctagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:9:8337:12329#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":6}}
|
||||
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:15:12854:18952#0/1_sub[28..126] {"count":10,"merged_sample":{"29a_F260619":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":16}}
|
||||
ttagccctaaacataagctattccataacaaaattattcgccagagtactaccggcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:1:4513:20277#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaaccattctataacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:57:18237:6765#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattatgcgccagagtactgccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:119:8691:15994#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcgat
|
||||
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:6:1739:11421#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgctagagtactactagcaaca
|
||||
gcctgacactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:73:17136:17728#0/1_sub[28..127] {"count":6,"merged_sample":{"13a_F730603":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaattattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:76:9874:3117#0/1_sub[28..127] {"count":9,"merged_sample":{"29a_F260619":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:18:16679:15889#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:52:6908:8410#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":10}}
|
||||
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:71:13461:7411#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagaagactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
|
||||
tttt
|
||||
>HELIUM_000100422_612GNAAXX:7:47:6989:13864#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:72:8941:18482#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggtggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:25:10818:13742#0/1_sub[28..133] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||
ttagccctaaacgtaaactgcaaactattccataataaaataattcgcccaagaactact
|
||||
agcaacagcttaaaactcaaaggacttggtggtgctttctacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:70:11509:6042#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagaaattaatataacaaaaatattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:46:4342:17317#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
|
||||
gcttaaaactcaaaggacttggcggtgccttacgtccct
|
||||
>HELIUM_000100422_612GNAAXX:7:111:17844:17230#0/1_sub[28..126] {"count":13,"merged_sample":{"26a_F040644":13},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":17}}
|
||||
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacgtggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:34:17680:16952#0/1_sub[28..127] {"count":15,"merged_sample":{"13a_F730603":15},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":15}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:34:2640:2539#0/1_sub[28..127] {"count":19,"merged_sample":{"29a_F260619":19},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":25}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:71:18891:9661#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacgtggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:26:16553:1613#0/1_sub[77..81] {"count":38,"merged_sample":{"13a_F730603":38},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":38}}
|
||||
caata
|
||||
>HELIUM_000100422_612GNAAXX:7:45:5732:11220#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggtggtgctttctacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:1:14254:1103#0/1_sub[28..126] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:50:17151:20608#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:96:13203:2879#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":6}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:78:18041:18996#0/1_sub[28..126] {"count":13,"merged_sample":{"13a_F730603":9,"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s"},"obiclean_weight":{"13a_F730603":9,"15a_F730814":4}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:80:18387:10166#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:100:14685:15065#0/1_sub[28..127]":"(a)->(t)@24","HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127]":"(t)->(g)@71"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:54:10113:12172#0/1_sub[28..127] {"count":7,"merged_sample":{"15a_F730814":4,"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":5,"29a_F260619":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:97:17822:18365#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatcccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:87:6328:12406#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:4611:13145#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacgtccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:78:6346:5817#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
|
||||
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:15122:17310#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:94:6384:20392#0/1_sub[28..127]":"(a)->(t)@52"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacttcctgcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:27:7695:17738#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:48:15379:13773#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
|
||||
ttagccctaaacatagataattttacaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:117:16246:17184#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":10}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:87:11044:6323#0/1_sub[28..126] {"count":69,"merged_sample":{"26a_F040644":69},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":84}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:40:12248:18615#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:6470:13562#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacctccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:72:11850:15705#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:82:8566:4827#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":9}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggtggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:43:16297:17399#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:15117:2564#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacctccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:90:4058:17862#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:43:13909:1377#0/1_sub[28..126] {"count":10,"merged_sample":{"26a_F040644":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":14}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:36:3584:21256#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaagctattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatgccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:80:13357:2959#0/1_sub[74..81] {"count":12,"merged_sample":{"29a_F260619":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
||||
ccgatagg
|
||||
>HELIUM_000100422_612GNAAXX:7:70:8097:4516#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaagaaacaagaatgttcaccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcagtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:8746:5790#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacctctagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:8:9165:18915#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactatgaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:85:7323:6139#0/1_sub[28..126] {"count":9,"merged_sample":{"26a_F040644":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":16}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:23:6103:3418#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:107:2103:10677#0/1_sub[28..127] {"count":20,"merged_sample":{"13a_F730603":20},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":22}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:1:15993:20360#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacctgcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatgccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:103:1205:6990#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ttagccctaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:111:2380:10482#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:76:10530:11312#0/1_sub[28..126] {"count":43,"merged_sample":{"26a_F040644":43},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":69}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:40:15984:4911#0/1_sub[28..126] {"count":16,"merged_sample":{"26a_F040644":16},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":30}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:109:19171:17424#0/1_sub[28..126] {"count":2,"merged_sample":{"13a_F730603":1,"26a_F040644":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126]":"(a)->(t)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s","26a_F040644":"i"},"obiclean_weight":{"13a_F730603":1,"26a_F040644":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggacttctagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:77:17898:19592#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaataattcgccagaggactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:32:4908:16517#0/1_sub[78..81] {"count":7,"merged_sample":{"29a_F260619":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
|
||||
ccgc
|
||||
>HELIUM_000100422_612GNAAXX:7:100:8022:19461#0/1_sub[28..127] {"count":5,"merged_sample":{"29a_F260619":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":11}}
|
||||
ttagccctaaacacaagtaattaatataacaaaataattcgccagagaactactagcaac
|
||||
agattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:59:2390:15297#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:98:10839:20244#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:34:13086:6440#0/1_sub[28..127] {"count":14,"merged_sample":{"13a_F730603":14},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":18}}
|
||||
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:73:10944:14101#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":3}}
|
||||
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:61:17561:21218#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:93:7569:17305#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcagtctataacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:55:11954:15731#0/1_sub[28..126] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:54:15067:12524#0/1_sub[28..126] {"count":26,"merged_sample":{"26a_F040644":26},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":49}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:6:10451:2548#0/1_sub[28..126] {"count":12,"merged_sample":{"26a_F040644":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":15}}
|
||||
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:23:10872:20213#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgccttacgtccct
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:98:6034:5203#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:70:2429:19509#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgccttacgtccct
|
||||
>HELIUM_000100422_612GNAAXX:7:65:1843:2567#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:92:1339:19811#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattacacaaacaaaattgttcacaagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:15:13855:1746#0/1_sub[28..127] {"count":3,"merged_sample":{"15a_F730814":2,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:7:14405:19348#0/1_sub[28..127]":"(t)->(g)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":3,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtgcgaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:7092:11003#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacgtccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
@@ -0,0 +1,24 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
@@ -0,0 +1,24 @@
|
||||
>seq0001 {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":1,"taxid":"taxon:9992 [Marmota]@genus"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>seq0002 {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","seq_number":2,"taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0003 {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":3,"taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0004 {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","seq_number":4,"taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>seq0005 {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","seq_number":5,"taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>seq0006 {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":6,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0007 {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":7,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0008 {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":8,"taxid":"taxon:9611 [Canis]@genus"}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
@@ -0,0 +1,9 @@
|
||||
id,count,obitag_bestid,obitag_bestmatch,obitag_match_count,obitag_rank,obitag_similarity_method,seq_number,taxid,sequence
|
||||
seq0001,10172,0.9797979797979798,AY227529,1,genus,lcs,1,taxon:9992 [Marmota]@genus,ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
seq0002,260,0.9405940594059405,AF154263,9,infraorder,lcs,2,taxon:35500 [Pecora]@infraorder,ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0003,7146,1,AB245427,1,species,lcs,3,taxon:9860 [Cervus elaphus]@species,ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0004,87,0.9494949494949495,AY227530,2,tribe,lcs,4,taxon:337730 [Marmotini]@tribe,ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
seq0005,95,0.9595959595959596,AC187326,1,subspecies,lcs,5,taxon:9615 [Canis lupus familiaris]@subspecies,ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
|
||||
seq0006,12004,1,AJ885202,1,species,lcs,6,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0007,319,1,AJ972683,1,species,lcs,7,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0008,366,1,AB048590,1,genus,lcs,8,taxon:9611 [Canis]@genus,ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
|
@@ -0,0 +1,6 @@
|
||||
id,seq0001,seq0002,seq0003,seq0004,seq0005,seq0006,seq0007,seq0008
|
||||
29a_F260619,0,337,0,0,105,5789,376,1
|
||||
15a_F730814,0,0,0,0,0,8822,0,5
|
||||
13a_F730603,0,0,8039,0,0,0,0,17
|
||||
26a_F040644,12205,0,0,202,12,0,0,468
|
||||
|
||||
|
@@ -0,0 +1,24 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 17 KiB |
Binary file not shown.
@@ -0,0 +1,8 @@
|
||||
@param,matching,strict
|
||||
@param,primer_mismatches,2
|
||||
@param,indels,false
|
||||
experiment,sample,sample_tag,forward_primer,reverse_primer
|
||||
wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
|
1530
jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
Normal file
1530
jupyterhub_volumes/web/obidoc/docs/cookbook/index.html
Normal file
File diff suppressed because it is too large
Load Diff
12
jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
Normal file
12
jupyterhub_volumes/web/obidoc/docs/cookbook/index.xml
Normal file
@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Cookbook on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/</link>
|
||||
<description>Recent content in Cookbook on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
@@ -0,0 +1,102 @@
|
||||
SHELL := /bin/bash
|
||||
FTPNCBI=ftp.ncbi.nlm.nih.gov
|
||||
GBURL=https://$(FTPNCBI)/genbank
|
||||
GBRELEASE_URL=$(GBURL)/GB_Release_Number
|
||||
|
||||
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
|
||||
|
||||
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
|
||||
|
||||
GBDIV_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E 'gb.+\.seq\.gz' \
|
||||
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
|
||||
| sort \
|
||||
| uniq)
|
||||
|
||||
GBDIV=bct inv mam phg pln pri rod vrl vrt
|
||||
DIRECTORIES=fasta fasta_fgs
|
||||
|
||||
GBFILE_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
|
||||
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
|
||||
|
||||
|
||||
SUFFIXES += .d
|
||||
NODEPS:=clean taxonomy
|
||||
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
|
||||
|
||||
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
|
||||
#Chances are, these files don't exist. GMake will create them and
|
||||
#clean up automatically afterwards
|
||||
-include $(DEPFILES)
|
||||
endif
|
||||
|
||||
|
||||
all: depends directories FORCE
|
||||
@make downloads
|
||||
|
||||
downloads: taxonomy fasta_files
|
||||
@echo Genbank Release number $(GBRELEASE)
|
||||
@echo all divisions : $(GBDIV_ALL)
|
||||
|
||||
FORCE:
|
||||
|
||||
.PHONY: all directories depends taxonomy fasta_files FORCE
|
||||
|
||||
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
|
||||
|
||||
division: $(GBDIV)
|
||||
|
||||
taxonomy: directories Release_$(GBRELEASE)/taxonomy
|
||||
|
||||
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
|
||||
|
||||
Release_$(GBRELEASE):
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
|
||||
@echo Create depends directory
|
||||
@mkdir -p Release_$(GBRELEASE)/depends
|
||||
@for f in ${GBFILE_ALL} ; do \
|
||||
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
|
||||
echo -e "\t@echo Downloading file : $$f..." ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
|
||||
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
|
||||
echo ; \
|
||||
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
|
||||
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_files="$$fasta_files $$fasta" ; \
|
||||
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
|
||||
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
|
||||
echo -e "\t@echo converting file : \$$< in fasta" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
|
||||
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
|
||||
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
|
||||
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
|
||||
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
|
||||
echo -e "\t || rm -f \$$@" ; \
|
||||
echo -e "\t@echo conversion of $$@ done." ; \
|
||||
echo ; \
|
||||
done > $@ ; \
|
||||
echo >> $@ ; \
|
||||
echo "fasta_files: $$fasta_files" >> $@ ;
|
||||
|
||||
Release_$(GBRELEASE)/taxonomy:
|
||||
mkdir -p $@
|
||||
curl -iL $(TAXOURL) \
|
||||
| tar -C $@ -zxf -
|
||||
1919
jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
Normal file
1919
jupyterhub_volumes/web/obidoc/docs/cookbook/local_genbank/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Prepare a local copy of Genbank on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/local_genbank/</link>
|
||||
<description>Recent content in Prepare a local copy of Genbank on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/local_genbank/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
1552
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
Normal file
1552
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.html
Normal file
File diff suppressed because it is too large
Load Diff
12
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
Normal file
12
jupyterhub_volumes/web/obidoc/docs/cookbook/minion/index.xml
Normal file
@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Oxford Nanopore data analysis on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/minion/</link>
|
||||
<description>Recent content in Oxford Nanopore data analysis on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/minion/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
1702
jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
Normal file
1702
jupyterhub_volumes/web/obidoc/docs/cookbook/reference_db/index.html
Normal file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Build a reference database on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/reference_db/</link>
|
||||
<description>Recent content in Build a reference database on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/reference_db/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
Reference in New Issue
Block a user