Hi, Andreas, على السبت 5 كانون الأول 2015 23:53، كتب Andreas Tille: > Hi, > > other uploaders of pysam in CC: When building htseq with current pysam > in unstable I get: >
[...] > File > "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line > 976, in __getitem__ > if not self.sf._hasIndex(): > AttributeError: 'pysam.csamfile.Samfile' object has no attribute > '_hasIndex' > ********************************************************************** [...] > File "<doctest tss.rst[29]>", line 1, in <module> > almnt.iv.length = fragmentsize > AttributeError: 'NoneType' object has no attribute 'length' > ********************************************************************** > File "../doc/tss.rst", line 221, in tss.rst > Failed example: > almnt > Expected: > <SAM_Alignment object: Read 'SRR001432.205754 > USI-EAS21_0008_3445:8:5:217:355 length=25' aligned to > 1:[145440800,145441000)/-> > Got: > <SAM_Alignment object: Read 'SRR001432.299973 > USI-EAS21_0008_3445:8:7:811:450 length=25', not aligned> > > ... > > NameError: name 'start_in_window' is not defined [...] > > Any idea how to fix this. Htslib upstream is unresponsive even to less > hard issues. > The recent pysam release dropped support for some deprecated interfaces and this package appears to have been affected. I can prepare a patch for those pysam issues as I did for pbcore [1] By the way, I had checked rdepends of pysam to look out for packages that may have problems later on due to the change, but the only way I know how to do that is using apt-cache rdepends. This has limitations because I use Stable and can't get an up-to-date report without changing my sources.list regards Afif 1. http://anonscm.debian.org/cgit/debian-med/python-pbcore.git/tree/debian/patches/fix-pysam-compatibility.patch which fixed http://bugs.debian.org/805687 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
