#!/usr/bin/python3 import struct import sys import os import gzip ##### # # Generic file function # ##### class Filter(object): def __init__(self,path): self._path = path self._taxonFile = "%s.tdx" % self._path self._ranksFile = "%s.rdx" % self._path self._namesFile = "%s.ndx" % self._path self._taxonomy, self._index, self._ranks, self._name = self.__readNodeTable() def __universalOpen(self,file): if isinstance(file,str): if file[-3:] == '.gz': rep = gzip.open(file) else: rep = open(file) else: rep = file return rep def __universalTell(self,file): if isinstance(file, gzip.GzipFile): file=file.myfileobj return file.tell() def __fileSize(self,file): if isinstance(file, gzip.GzipFile): file=file.myfileobj pos = file.tell() file.seek(0,2) length = file.tell() file.seek(pos,0) return length def __progressBar(self,pos,max,reset=False,delta=[]): if reset: del delta[:] if not delta: delta.append(time.time()) delta.append(time.time()) delta[1]=time.time() elapsed = delta[1]-delta[0] percent = float(pos)/max * 100 remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent))) bar = '#' * int(percent/2) bar+= '|/-\\-'[pos % 5] bar+= ' ' * (50 - int(percent/2)) sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain)) ##### # # Iterator functions # ##### def __ecoRecordIterator(self,file): file = self.__universalOpen(file) (recordCount,) = struct.unpack('> I',file.read(4)) for i in range(recordCount): (recordSize,)=struct.unpack('>I',file.read(4)) record = file.read(recordSize) yield record def __ecoNameIterator(self): for record in self.__ecoRecordIterator(self._namesFile): lrecord = len(record) lnames = lrecord - 16 (isScientificName,namelength,classLength,indextaxid,names)=struct.unpack('> I I I I %ds' % lnames, record) name=names[:namelength] classname=names[namelength:] yield (name,classname,indextaxid) def __ecoTaxonomicIterator(self): for record in self.__ecoRecordIterator(self._taxonFile): lrecord = len(record) lnames = lrecord - 16 (taxid,rankid,parentidx,nameLength,name)=struct.unpack('> I I I I %ds' % lnames, record) yield (taxid,rankid,parentidx,name) def __ecoSequenceIterator(self,file): for record in self.__ecoRecordIterator(file): lrecord = len(record) lnames = lrecord - (4*4+20) (taxid,seqid,deflength,seqlength,cptseqlength,string)=struct.unpack('> I 20s I I I %ds' % lnames, record) de = string[:deflength] seq = gzip.zlib.decompress(string[deflength:]) yield (taxid,seqid,deflength,seqlength,cptseqlength,de,seq) def __ecoRankIterator(self): for record in self.__ecoRecordIterator(self._ranksFile): yield record ##### # # Indexes # ##### def __ecoNameIndex(self): indexName = [x for x in self.__ecoNameIterator()] return indexName def __ecoRankIndex(self): rank = [r for r in self.__ecoRankIterator()] return rank def __ecoTaxonomyIndex(self): taxonomy = [] index = {} i = 0; for x in self.__ecoTaxonomicIterator(): taxonomy.append(x) index[x[0]] = i i = i + 1 return taxonomy, index def __readNodeTable(self): taxonomy, index = self.__ecoTaxonomyIndex() ranks = self.__ecoRankIndex() name = self.__ecoNameIndex() return taxonomy,index,ranks,name def findTaxonByTaxid(self,taxid): return self._taxonomy[self._index[taxid]] ##### # # PUBLIC METHODS # ##### def subTreeIterator(self, taxid): "return subtree for given taxonomic id " idx = self._index[taxid] yield self._taxonomy[idx] for t in self._taxonomy: if t[2] == idx: for subt in self.subTreeIterator(t[0]): yield subt def parentalTreeIterator(self, taxid): """ return parental tree for given taxonomic id starting from first ancester to the root. """ taxon=self.findTaxonByTaxid(taxid) while taxon[2]!= 0: yield taxon taxon = self._taxonomy[taxon[2]] yield self._taxonomy[0] def ecoPCRResultIterator(self, file): "iteration on ecoPCR result file" file = self.__universalOpen(file) data = ColumnFile(file, sep='|', types=(str,int,int, str,int,str, int,str,int, str,int,str, str,str,int, str,int,int, str,str),skip='#') for ac, sq_len, taxid,\ rank, sp_taxid, species,\ ge_taxid, genus, fa_taxid,\ family, sk_taxid, s_kgdom,\ strand, oligo_1, error_1,\ oligo_2, error_2, amp_len,\ sq_des, definition in data: yield {'ac':ac, 'sq_len':sq_len, 'taxid':taxid, 'rank':rank, 'sp_taxid':sp_taxid, 'species':species, 'ge_taxid':ge_taxid, 'genus':genus, 'fa_taxid':fa_taxid, 'family':family, 'sk_taxid':sk_taxid, 's_kgdom':s_kgdom, 'strand':strand, 'oligo_1':oligo_1, 'error_1':error_1, 'oligo_2':oligo_2, 'error_2':error_2, 'amp_len':amp_len, 'sq_des':sq_des, 'definition':definition} def rankFilter(self,rankid,filter): return self._ranks[rankid] == filter def lastCommonTaxon(self,taxid_1, taxid_2): t1 = [x[0] for x in self.parentalTreeIterator(taxid_1)] t2 = [x[0] for x in self.parentalTreeIterator(taxid_2)] t1.reverse() t2.reverse() count = t1 < t2 and len(t1) or len(t2) for i in range(count): if t1[i] != t2[i]: return t1[i-1] class ColumnFile(object): def __init__(self,stream,sep=None,strip=True,types=None,skip=None): if isinstance(stream,str): self._stream = open(stream) elif hasattr(stream,'next'): self._stream = stream else: raise ValueError('stream must be string or an iterator') self._delimiter=sep self._strip=strip if types: self._types=[x for x in types] for i in range(len(self._types)): if self._types[i] is bool: self._types[i]=ColumnFile.str2bool else: self._types=None self._skip = skip def str2bool(x): return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False})) str2bool = staticmethod(str2bool) def __iter__(self): return self def __next__(self): ligne = next(self._stream) while ligne[0] == self._skip: ligne = next(self._stream) data = ligne.split(self._delimiter) if self._strip or self._types: data = [x.strip() for x in data] if self._types: it = self.endLessIterator(self._types) data = [x[1](x[0]) for x in ((y,next(it)) for y in data)] return data def endLessIterator(self,endedlist): for x in endedlist: yield x while(1): yield endedlist[-1] class Table(list): def __init__(self, headers, types): list.__init__(self) self.headers = headers self.types = types self.lines = [] def printTable(self): for h in self.headers: print("\t%s\t|" % h, end=' ') print("\n") for l in self.lines: for c in l: print("\t%s\t|" % c) print("\n") def getColumn(self,n): print("\t%s\n" % self.header[n]) for i in range(len(self.lines)): print("\t%s\n" % i[n])