Merge of eric-test branche to the trunk
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@200 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
651
tools/ecoPCRFormat.py
Executable file
651
tools/ecoPCRFormat.py
Executable file
@ -0,0 +1,651 @@
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#!/usr/bin/env python
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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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try:
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import psycopg2
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_dbenable=True
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except ImportError:
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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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elif hasattr(stream,'next'):
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self._stream = stream
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else:
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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 xrange(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 = self._stream.next()
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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,it.next()) 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 = 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 = (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 >>sys.stderr,"Reading taxonomy dump file..."
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taxonomy=[[n[0],n[2],n[1]] for n in nodes]
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print >>sys.stderr,"List all taxonomy rank..."
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ranks =list(set(x[1] for x in taxonomy))
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ranks.sort()
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ranks = dict(map(None,ranks,xrange(len(ranks))))
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print >>sys.stderr,"Sorting taxons..."
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taxonomy.sort(taxonCmp)
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print >>sys.stderr,"Indexing taxonomy..."
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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 >>sys.stderr,"Indexing parent and rank..."
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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 >>sys.stderr,"Adding scientific name..."
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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 >>sys.stderr,"Adding taxid alias..."
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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 >>sys.stderr,"Adding deleted taxid..."
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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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def readTaxonomyDB(dbname):
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connection = psycopg2.connect(database=dbname)
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cursor = connection.cursor()
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cursor.execute("select numid,rank,parent from ncbi_taxonomy.taxon")
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taxonomy=[list(x) for x in cursor]
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cursor.execute("select rank_class from ncbi_taxonomy.taxon_rank_class order by rank_class")
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ranks=cursor.fetchall()
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ranks = dict(map(None,(x[0] for x in ranks),xrange(len(ranks))))
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print >>sys.stderr,"Sorting taxons..."
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taxonomy.sort(taxonCmp)
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print >>sys.stderr,"Indexing taxonomy..."
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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 >>sys.stderr,"Indexing parent and rank..."
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for t in taxonomy:
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t[1]=ranks[t[1]]
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try:
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t[2]=index[t[2]]
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except KeyError,e:
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if t[2] is None and t[0]==1:
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t[2]=index[t[0]]
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else:
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raise e
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cursor.execute("select taxid,name,category from ncbi_taxonomy.name")
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alternativeName=[]
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for taxid,name,classname in cursor:
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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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cursor.execute("select old_numid,current_numid from ncbi_taxonomy.taxon_id_alias")
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print >>sys.stderr,"Adding taxid alias..."
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for taxid,current in cursor:
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if current is not None:
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index[taxid]=index[current]
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else:
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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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for ligne in file:
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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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def fastaEntryIterator(file):
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file = universalOpen(file)
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rep =[]
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for ligne in file:
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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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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)
|
||||
if Tx is not None:
|
||||
Tx=int(Tx)
|
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return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
|
||||
|
||||
|
||||
def sequenceIteratorFactory(entryParser,entryIterator):
|
||||
def sequenceIterator(file):
|
||||
for entry in entryIterator(file):
|
||||
yield entryParser(entry)
|
||||
return sequenceIterator
|
||||
|
||||
|
||||
def taxonomyInfo(entry,connection):
|
||||
taxid = entry['taxid']
|
||||
curseur = connection.cursor()
|
||||
curseur.execute("""
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||||
select taxid,species,genus,family,
|
||||
taxonomy.scientificName(taxid) as sn,
|
||||
taxonomy.scientificName(species) as species_sn,
|
||||
taxonomy.scientificName(genus) as genus_sn,
|
||||
taxonomy.scientificName(family) as family_sn
|
||||
from
|
||||
(
|
||||
select alias as taxid,
|
||||
taxonomy.getSpecies(alias) as species,
|
||||
taxonomy.getGenus(alias) as genus,
|
||||
taxonomy.getFamily(alias) as family
|
||||
from taxonomy.aliases
|
||||
where id=%d ) as tax
|
||||
""" % taxid)
|
||||
rep = curseur.fetchone()
|
||||
entry['current_taxid']=rep[0]
|
||||
entry['species']=rep[1]
|
||||
entry['genus']=rep[2]
|
||||
entry['family']=rep[3]
|
||||
entry['scientific_name']=rep[4]
|
||||
entry['species_sn']=rep[5]
|
||||
entry['genus_sn']=rep[6]
|
||||
entry['family_sn']=rep[7]
|
||||
return entry
|
||||
|
||||
#####
|
||||
#
|
||||
#
|
||||
# Binary writer
|
||||
#
|
||||
#
|
||||
#####
|
||||
|
||||
def ecoSeqPacker(sq):
|
||||
|
||||
compactseq = gzip.zlib.compress(sq['sequence'],9)
|
||||
cptseqlength = len(compactseq)
|
||||
delength = len(sq['definition'])
|
||||
|
||||
totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
|
||||
|
||||
packed = struct.pack('> I I 20s I I I %ds %ds' % (delength,cptseqlength),
|
||||
totalSize,
|
||||
sq['taxid'],
|
||||
sq['id'],
|
||||
delength,
|
||||
len(sq['sequence']),
|
||||
cptseqlength,
|
||||
sq['definition'],
|
||||
compactseq)
|
||||
|
||||
assert len(packed) == totalSize+4, "error in sequence packing"
|
||||
|
||||
return packed
|
||||
|
||||
def ecoTaxPacker(tx):
|
||||
|
||||
namelength = len(tx[3])
|
||||
|
||||
totalSize = 4 + 4 + 4 + 4 + namelength
|
||||
|
||||
packed = struct.pack('> I I I I I %ds' % namelength,
|
||||
totalSize,
|
||||
tx[0],
|
||||
tx[1],
|
||||
tx[2],
|
||||
namelength,
|
||||
tx[3])
|
||||
|
||||
return packed
|
||||
|
||||
def ecoRankPacker(rank):
|
||||
|
||||
namelength = len(rank)
|
||||
|
||||
packed = struct.pack('> I %ds' % namelength,
|
||||
namelength,
|
||||
rank)
|
||||
|
||||
return packed
|
||||
|
||||
def ecoNamePacker(name):
|
||||
|
||||
namelength = len(name[0])
|
||||
classlength= len(name[1])
|
||||
totalSize = namelength + classlength + 4 + 4 + 4 + 4
|
||||
|
||||
packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
|
||||
totalSize,
|
||||
int(name[1]=='scientific name'),
|
||||
namelength,
|
||||
classlength,
|
||||
name[2],
|
||||
name[0],
|
||||
name[1])
|
||||
|
||||
return packed
|
||||
|
||||
def ecoSeqWriter(file,input,taxindex,parser):
|
||||
output = open(file,'wb')
|
||||
input = universalOpen(input)
|
||||
inputsize = fileSize(input)
|
||||
entries = parser(input)
|
||||
seqcount=0
|
||||
skipped = []
|
||||
|
||||
output.write(struct.pack('> I',seqcount))
|
||||
|
||||
progressBar(1, inputsize,reset=True)
|
||||
for entry in entries:
|
||||
if entry['taxid'] is not None:
|
||||
try:
|
||||
entry['taxid']=taxindex[entry['taxid']]
|
||||
except KeyError:
|
||||
entry['taxid']=None
|
||||
if entry['taxid'] is not None:
|
||||
seqcount+=1
|
||||
output.write(ecoSeqPacker(entry))
|
||||
else:
|
||||
skipped.append(entry['id'])
|
||||
where = universalTell(input)
|
||||
progressBar(where, inputsize)
|
||||
print >>sys.stderr," Readed sequences : %d " % seqcount,
|
||||
else:
|
||||
skipped.append(entry['id'])
|
||||
|
||||
print >>sys.stderr
|
||||
output.seek(0,0)
|
||||
output.write(struct.pack('> I',seqcount))
|
||||
|
||||
output.close()
|
||||
return skipped
|
||||
|
||||
|
||||
def ecoTaxWriter(file,taxonomy):
|
||||
output = open(file,'wb')
|
||||
output.write(struct.pack('> I',len(taxonomy)))
|
||||
|
||||
for tx in taxonomy:
|
||||
output.write(ecoTaxPacker(tx))
|
||||
|
||||
output.close()
|
||||
|
||||
def ecoRankWriter(file,ranks):
|
||||
output = open(file,'wb')
|
||||
output.write(struct.pack('> I',len(ranks)))
|
||||
|
||||
rankNames = ranks.keys()
|
||||
rankNames.sort()
|
||||
|
||||
for rank in rankNames:
|
||||
output.write(ecoRankPacker(rank))
|
||||
|
||||
output.close()
|
||||
|
||||
def nameCmp(n1,n2):
|
||||
name1=n1[0].upper()
|
||||
name2=n2[0].upper()
|
||||
if name1 < name2:
|
||||
return -1
|
||||
elif name1 > name2:
|
||||
return 1
|
||||
return 0
|
||||
|
||||
|
||||
def ecoNameWriter(file,names):
|
||||
output = open(file,'wb')
|
||||
output.write(struct.pack('> I',len(names)))
|
||||
|
||||
names.sort(nameCmp)
|
||||
|
||||
for name in names:
|
||||
output.write(ecoNamePacker(name))
|
||||
|
||||
output.close()
|
||||
|
||||
def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
|
||||
|
||||
ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
|
||||
ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
|
||||
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 >>sys.stderr,"Skipped entry :"
|
||||
print >>sys.stderr,sk
|
||||
|
||||
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:])
|
||||
|
||||
if opt['taxmod']=='dump':
|
||||
taxonomy = readTaxonomyDump(opt['taxdir'])
|
||||
elif opt['taxmod']=='db':
|
||||
taxonomy = readTaxonomyDB(opt['taxdb'])
|
||||
|
||||
|
||||
ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
|
||||
|
||||
Reference in New Issue
Block a user