HTSeq test case failures

[Diane Trout <diane@ghic.org>]

Hello,

I had time to make more progress on improving the debian HTSeq package, and 
have updated it to run your test code.

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.

Diane Trout


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 '-'>])
**********************************************************************