bam_stat.py error

[Yuan Hao]

Hi,

I just installed the RSeQC-2.3.9 and try to test bam_stat.py. I tried either signle- or paired-end bam files mapped by bowtie 2. I constantly got the following error messages.Do you have any idea what might be the cause? Should I sort the files in advance? Thanks!

$ bam_stat.py -i test.bam 

Traceback (most recent call last):

  File "/home/.local/bin/bam_stat.py", line 5, in <module>

    pkg_resources.run_script('RSeQC==2.3.9', 'bam_stat.py')

  File "/home/.local/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 505, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/home/.local/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 1245, in run_script

    execfile(script_filename, namespace, namespace)

  File "/home/.local/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/bam_stat.py", line 63, in <module>

    main()

  File "/home/.local/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/EGG-INFO/scripts/bam_stat.py", line 59, in main

    obj.stat(q_cut = options.map_qual)

AttributeError: ParseBAM instance has no attribute 'stat'

[Liguo Wang]

I double checked. ParseBAM module indeed has the 'stat' function.

If you have installed older version of RSeQC (or EVER-seq), please remove them completely from your "/.../site-packages" folder (the reason is that older module which does NOT have "stat" function might override the most recent version). 

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[Yuan Hao]

Hi there,

Thanks a million for the info. Problem resolved!

Cheers,

Yuan