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DoaneAS / rseqc

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insert_size calculation #1

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
using

inner_distance.py -i accepted_hits.bam -o insert_size -r $exons_gtf

I expect an out file with the fragment size distribution

but i get this error

/../install_lib/RSeQC/RSeQC-2.0.0/bin/Archive/Software/PYTHON/python-2.6.4/bin/i
nner_distance.py:15: DeprecationWarning: the sets module is deprecated
import sets
Traceback (most recent call last):
File 
"/../install_lib/RSeQC/RSeQC-2.0.0/bin/Archive/Software/PYTHON/python-2.6.4/bin/
inner_distance.py", line 75, in <module>
main()
File 
"/../install_lib/RSeQC/RSeQC-2.0.0/bin/Archive/Software/PYTHON/python-2.6.4/bin/
inner_distance.py", line 70, in main
obj = SAM.ParseBAM(options.input_file)
AttributeError: 'module' object has no attribute 'ParseBAM'

thanks

M.

Original issue reported on code.google.com by mauro.p...@bioflag.it on 30 Mar 2012 at 5:21

GoogleCodeExporter commented 9 years ago 
I get the same error (AttributeError: 'module' object has no attribute 
'ParseBAM') for bam_stat.py.

Thanks

Pascal

Original comment by androidp...@gmail.com on 13 Apr 2012 at 9:07

GoogleCodeExporter commented 9 years ago 
Sorry guys. I didn't see this issue till now. 
Unfortunately, I cannot repeat your problems. Could you please download the 
newer version and try a again?

http://code.google.com/p/rseqc/downloads/list

I guess the error is because that PYTHONPATH was not set properly. You can do 
it explicitly:
for example:
$ export 
PYTHONPATH=/home/user/tools/RSeQC2/usr/local/lib/python2.7/site-packages

Email me directly if you still have questions.

wangliguo78 AT gmail.com

Thanks for using RSeQC

-Liguo

Original comment by wangligu...@gmail.com on 19 Apr 2012 at 6:32