[BioC] Where is DEXSeq bioconductor package?

[Fabrice Tourre]

When I run python script dexseq_count.py in DEXseq. I have these error.

~/bin/python/python /env/ins/home/user/bin/dexseq_count.py -p yes -s
yes -a 10 /env/ins/home/user/rna-seq/info/DEX-63.gtf
~/rna-seq/exp/data/mapping/bwa/7005_4.sam test.count

/env/ins/home/user/bin/python/lib/python2.7/site-packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543:
UserWarning: Malformed SAM line: MRNM != '*' although flag bit &0x0008
set
  algnt = SAM_Alignment.from_SAM_line( line )
/env/ins/home/user/bin/python/lib/python2.7/site-packages/HTSeq-0.5.3p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py:543:
UserWarning: Malformed SAM line: RNAME != '*' although flag bit
&0x0004 set
  algnt = SAM_Alignment.from_SAM_line( line )
Traceback (most recent call last):
  File "/env/ins/home/user/bin/rnaseq/pipeline/dexseq_count.py", line
138, in <module>
    counts[ '_loqaqual' ] += 1
KeyError: '_loqaqual'


Python:2.7
HTSeq:0.5.3p1
DEXseq:0.1.12
Sam produced by bwa (bwa-0.5.9) against Ensembl 63 (Human, RNA-seq
pair-end sample).
It seems that BWA convert all the reads to forward strand, so I set -s
yes. Is it right?

Thank you.