htseq-qa AttributeError

[Libra66]

Dear all,

I get an error message when trying to call htseq-qa (version 0.8.0, see below).

The program was called from Ubuntu 16.04 LTS. htseq-count works well on this system.

When I carry out htseq-qa (version 0.6.0) from our cluster computer (Liunx SLES) on the same sam file it works well.

What could be the reason for the error message below?

Libra66@pc65472:/data/bowtie_workflow$ htseq-qa SRR1619533.sam

Error occured in: file SRR1619533.sam closed

Traceback (most recent call last):

File "/home/Libra66/.local/bin/htseq-qa", line 4, in import('pkg_resources').run_script('HTSeq==0.8.0', 'htseq-qa')

File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 719, in run_script self.require(requires)[0].run_script(script_name, ns)

File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 1504, in run_script exec(code, namespace, namespace)

File "/home/Libra66/.local/lib/python2.7/site-packages/HTSeq-0.8.0-py2.7-l inux -x86_64.egg/EGG-INFO/scripts/htseq-qa", line 5, in HTSeq.scripts.qa.main()

File "/home/Libra66/.local/lib/python2.7/site-packages/HTSeq-0.8.0-py2.7-l inux -x86_64.egg/HTSeq/scripts/qa.py", line 136, in main r.add_bases_to_count_array( base_arr_A )

AttributeError: 'HTSeq._HTSeq.SAM_Alignment' object has no attribute 'add_bases_to_count_array'

[iosonofabio]

I'll try and have a look, htseq-qa is not very popular hence the lack of proper testing.

[iosonofabio]

Ok I linted the script, now let's try and guess the error.

Edit: ok I can reproduce here, working on it...

[iosonofabio]

Found it, fixed in 831e450, closing