Re: HTSeq test case failures
[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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