#4 run example error

[Anonymous]

Originally created by: nature.h... (code.google.com)@gmail.com

What steps will reproduce the problem?
I got two problems in test example, I have run the two command line.
1. python REDItoolDnaRna.py -i rna.bam -j dna.bam -f reference.fa -o reditool-test -c 10,1 -Q 33,64 -q 25,25 -m 20,20 -s 2 -g 1 -u -a 6-0 -v 2 -n0.0 -N0.0 -V -t 3 &

2. REDItoolDenovo.py -i rna.bam -f reference.fa -o reditool-test -c 10 -Q 33 -q 25 -m 20 -s 2 -g 1 -T 6-0 -v 2 -n0.0 -V 0.05 &

What is the expected output? What do you see instead?
for the first command line, I got the STDERR as follow:
Script time --> START: 27/01/2015 15:21:01
Analysis ID: 415640044
Analysis on 1 regions.
Started analysis on region: chr21
Process Process-1:
Traceback (most recent call last):
  File "/home/username/software/Python-2.7.5/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/home/username/software/Python-2.7.5/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/username/software/REDItools-1.0.3/reditools/REDItoolDnaRna.py", line 1056, in do_work
    exploreBAM(x)
  File "/home/username/software/REDItools-1.0.3/reditools/REDItoolDnaRna.py", line 835, in exploreBAM
    gs,gq,gt,gqq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-gQVAL,'*',pileupread.alignment.qual[pileupread.qpos]
AttributeError: 'pysam.calignmentfile.PileupRead' object has no attribute 'qpos'
Merging Tables.
Results saved on reditool-test/DnaRna_415640044/outTable_415640044
Script time --> END: 27/01/2015 15:21:03

##########
for the second command line, I got:
Traceback (most recent call last):
  File "/home/username/software/REDItools-1.0.3/reditools/REDItoolDenovo.py", line 449, in <module>
    assert False, "Unhandled Option"
AssertionError: Unhandled Option

What version of the product are you using? On what operating system?
REDItools-1.0.3
CentOS release 6.5 (Final)

Please provide any additional information below.
I have read the documentions in http://150.145.82.212/ernesto/reditools/doc/
for the first problem I have re-install the pysam module. But it isn't work.
for the second problem I have check the REDItoolDenovo.py script from 378 to 450,
it looks like lose some code.

[Anonymous]

Originally posted by: nature.h... (code.google.com)@gmail.com

Following Dr. Ernesto suggestions, I changed my pysam version to pysam-0.7.7, it works great for the first question.(it might be caused the version of my pysam.)
For the second question, I made a modified on line 402 and 403 of the REDItoolDenovo.py scripts, I think it should be"
elif o == "-m": MAPQ=int(a)   
elif o == "-O": homo=int(a)
", and it works OK on my CentOS 6.5 with python 2.7.
Thanks to Dr. Ernesto again!