obitools/ecopcr
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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@85 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2007-06-29 07:14:53 +00:00
parent cacd9854f3
commit 8eccd87035
1 changed files with 3 additions and 5 deletions
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4
tools/ecoPCRFormat.py
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@ -69,7 +69,6 @@ def endLessIterator(endedlist):
while(1): while(1):
yield endedlist[-1] yield endedlist[-1]
class ColumnFile(object): class ColumnFile(object):
def __init__(self,stream,sep=None,strip=True,types=None): def __init__(self,stream,sep=None,strip=True,types=None):
@ -149,7 +148,6 @@ def readNodeTable(file):
bool,bool,bool,str)) bool,bool,bool,str))
print >>sys.stderr,"Reading taxonomy dump file..." print >>sys.stderr,"Reading taxonomy dump file..."
taxonomy=[[n[0],n[2],n[1]] for n in nodes] taxonomy=[[n[0],n[2],n[1]] for n in nodes]
print >>sys.stderr,"List all taxonomy rank..." print >>sys.stderr,"List all taxonomy rank..."
ranks =list(set(x[1] for x in taxonomy)) ranks =list(set(x[1] for x in taxonomy))
ranks.sort() ranks.sort()
@ -292,6 +290,7 @@ def emblEntryParser(entry):
Tx = None Tx = None
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq} return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
###################### ######################
def parseFasta(seq): def parseFasta(seq):
@ -315,7 +314,6 @@ def fastaEntryParser(entry):
return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq} return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
def sequenceIteratorFactory(entryParser,entryIterator): def sequenceIteratorFactory(entryParser,entryIterator):
def sequenceIterator(file): def sequenceIterator(file):
for entry in entryIterator(file): for entry in entryIterator(file):