Hi Diane,
the freeze is approaching quickly. Can you give any update of the state
of htseq?
Kind regards
Andreas.
On Fri, Jun 13, 2014 at 10:52:34AM +0200, Andreas Tille wrote:
> [Debian Science list in CC hoping for extra input about testing with
> differences caused by rounding]
>
> Hi Diane,
>
> On Thu, Jun 12, 2014 at 02:51:22PM -0700, Diane Trout wrote:
> > I had time to make more progress on improving the debian HTSeq package, and
> > have updated it to run your test code.
>
> Thanks. I really appreciate the effort to add tests and I try to
> approach this for all packages where upstream provides a test suite.
>
> > Unfortunately I had some test case failures. I was wondering if the tests
> > are
> > failing for you, or if its something about my configuration. Below is the
> > relevant error messages.
> >
> > One change from your code was I changed added
> >
> > import matplotlib
> > matplotlib.user('agg')
> >
> > to the start of test/test.py and test/tss_test.py to avoid an error I was
> > getting when trying to import _TkAgg.
> >
> > I'm using HTSeq 0.6.1p1 and pysam 0.7.7.
>
> I builded the package from Git (on amd64, rescent pbuilder unstable
> chroot) and had quite the same result as you. I'm afraid it depends from
> architecture and used compiler whether these tests might pass or fail but
> I'm lacking qualified experience.
>
> Any ideas?
>
> Kind regards
>
> Andreas.
>
> > Doctest of tss.rst:
> > **********************************************************************
> > File "../doc/tss.rst", line 52, in tss.rst
> > Failed example:
> > for feature in itertools.islice( gtffile, 100):
> > if feature.type == "exon" and feature.attr["exon_number"] == "1":
> > print feature.attr["gene_id"], feature.attr["transcript_id"],
> > feature.iv.start_d_as_pos
> > Expected:
> > ENSG00000223972 ENST00000456328 1:11873/+
> > ENSG00000223972 ENST00000450305 1:12009/+
> > ENSG00000227232 ENST00000423562 1:29368/-
> > ENSG00000227232 ENST00000438504 1:29368/-
> > ENSG00000227232 ENST00000488147 1:29568/-
> > ENSG00000227232 ENST00000430492 1:29341/-
> > ENSG00000243485 ENST00000473358 1:29553/+
> > ENSG00000243485 ENST00000469289 1:30266/+
> > ENSG00000221311 ENST00000408384 1:30365/+
> > ENSG00000237613 ENST00000417324 1:36079/-
> > ENSG00000237613 ENST00000461467 1:36071/-
> > ENSG00000233004 ENST00000421949 1:53048/+
> > ENSG00000240361 ENST00000492842 1:62947/+
> > ENSG00000177693 ENST00000326183 1:69054/+
> > Got:
> > ENSG00000223972 ENST00000456328 1:11873/+
> > ENSG00000223972 ENST00000450305 1:12009/+
> > ENSG00000227232 ENST00000423562 1:29369/-
> > ENSG00000227232 ENST00000438504 1:29369/-
> > ENSG00000227232 ENST00000488147 1:29569/-
> > ENSG00000227232 ENST00000430492 1:29342/-
> > ENSG00000243485 ENST00000473358 1:29553/+
> > ENSG00000243485 ENST00000469289 1:30266/+
> > ENSG00000221311 ENST00000408384 1:30365/+
> > ENSG00000237613 ENST00000417324 1:36080/-
> > ENSG00000237613 ENST00000461467 1:36072/-
> > ENSG00000233004 ENST00000421949 1:53048/+
> > ENSG00000240361 ENST00000492842 1:62947/+
> > ENSG00000177693 ENST00000326183 1:69054/+
> > **********************************************************************
> > File "../doc/tss.rst", line 313, in tss.rst
> > Failed example:
> > len( list( tssarray.chrom_vectors["1"]["."].steps() ) )
> > Expected:
> > 30089
> > Got:
> > 30085
> > **********************************************************************
> > File "../doc/tss.rst", line 338, in tss.rst
> > Failed example:
> > for step_iv, step_set in tssarray[ almnt.iv ].steps():
> > print "Step", step_iv, ", contained by these windows:"
> > for p in step_set:
> > print " Window around TSS at", p
> > Expected:
> > Step 1:[169677680,169677837)/. , contained by these windows:
> > Window around TSS at 1:169679671/-
> > Window around TSS at 1:169677779/-
> > Step 1:[169677837,169677880)/. , contained by these windows:
> > Window around TSS at 1:169680837/-
> > Window around TSS at 1:169679671/-
> > Window around TSS at 1:169677779/-
> > Got:
> > Step 1:[169677680,169677838)/. , contained by these windows:
> > Window around TSS at 1:169677780/-
> > Window around TSS at 1:169679672/-
> > Step 1:[169677838,169677880)/. , contained by these windows:
> > Window around TSS at 1:169680838/-
> > Window around TSS at 1:169679672/-
> > Window around TSS at 1:169677780/-
> > **********************************************************************
> > File "../doc/tss.rst", line 359, in tss.rst
> > Failed example:
> > s ##doctest:+NORMALIZE_WHITESPACE
> > Expected:
> > set([<GenomicPosition object '1':169680837, strand '-'>,
> > <GenomicPosition object '1':169677779, strand '-'>,
> > <GenomicPosition object '1':169679671, strand '-'>])
> > Got:
> > set([<GenomicPosition object '1':169680838, strand '-'>,
> > <GenomicPosition
> > object '1':169677780, strand '-'>, <GenomicPosition object '1':169679672,
> > strand '-'>])
> > **********************************************************************
> >
> >
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