diff --git a/tools/ecoPCRFormat.py b/tools/ecoPCRFormat.py index b28cda5..3acb26c 100755 --- a/tools/ecoPCRFormat.py +++ b/tools/ecoPCRFormat.py @@ -68,8 +68,7 @@ def endLessIterator(endedlist): yield x while(1): yield endedlist[-1] - - + class ColumnFile(object): def __init__(self,stream,sep=None,strip=True,types=None): @@ -135,7 +134,7 @@ def bsearchTaxon(taxonomy,taxid): else: return None - + def readNodeTable(file): @@ -149,7 +148,6 @@ def readNodeTable(file): bool,bool,bool,str)) print >>sys.stderr,"Reading taxonomy dump file..." taxonomy=[[n[0],n[2],n[1]] for n in nodes] - print >>sys.stderr,"List all taxonomy rank..." ranks =list(set(x[1] for x in taxonomy)) ranks.sort() @@ -292,6 +290,7 @@ def emblEntryParser(entry): Tx = None return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq} + ###################### def parseFasta(seq): @@ -315,7 +314,6 @@ def fastaEntryParser(entry): return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq} - def sequenceIteratorFactory(entryParser,entryIterator): def sequenceIterator(file): for entry in entryIterator(file):