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Old 04-20-2012, 06:49 AM   #1
greener
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Location: Seattle, WA

Join Date: Sep 2010
Posts: 17
Default errors while using python dexseq_prepare_annotation.py

Hi there, I am trying to use the dexseq_prepare_annotation.py tool in DEXseq and have tried several different gtf files but they all seem to get the same error. Not sure what could be causing this (below). Python version maybe? Any suggestions folks have are appreciated. Thanks -Rich

python dexseq_prepare_annotation.py test.gtf

Traceback (most recent call last):
File "dexseq_prepare_annotation.py", line 25, in ?
for f in HTSeq.GFF_Reader( gtf_file ):
File "/usr/lib64/python2.4/site-packages/HTSeq-0.5.3p3-py2.4-linux-x86_64.egg/HTSeq/__init__.py", line 204, in __iter__
for line in FileOrSequence.__iter__( self ):
File "/usr/lib64/python2.4/site-packages/HTSeq-0.5.3p3-py2.4-linux-x86_64.egg/HTSeq/__init__.py", line 42, in __iter__
if self.fos.lower().endswith( ( ".gz" , ".gzip" ) ):
TypeError: expected a character buffer object
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