biopython/biopython — pull request #186 by pgarland (2013-06-13 06:33:08+00:00)
Title: Add the new Bio.motifs.jaspar package to the list of packages to install

The new jaspar package wasn't being installed, causing these errors when running 'python setup.py test':

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ERROR: test_doctests (test_Tutorial.TutorialTestCase)
Run tutorial doctests.
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Traceback (most recent call last):
File "test_Tutorial.py", line 152, in test_doctests
ValueError: 1 Tutorial doctests failed: test_from_line_11404

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ERROR: test_simple (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works.
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Traceback (most recent call last):
File "test_motifs.py", line 1610, in setUp
self.m = motifs.read(handle, "pfm")
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 128, in read
motifs = parse(handle, format)
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 79, in parse
from Bio.motifs import jaspar
ImportError: cannot import name jaspar

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ERROR: test_pfm_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style pfm files.
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Traceback (most recent call last):
File "test_motifs.py", line 399, in test_pfm_parsing
m = motifs.read(self.PFMin, "pfm")
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 128, in read
motifs = parse(handle, format)
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 79, in parse
from Bio.motifs import jaspar
ImportError: cannot import name jaspar

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ERROR: test_sites_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style sites files.
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Traceback (most recent call last):
File "test_motifs.py", line 405, in test_sites_parsing
m = motifs.read(self.SITESin,"sites")
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 128, in read
motifs = parse(handle, format)
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 79, in parse
from Bio.motifs import jaspar
ImportError: cannot import name jaspar

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FAIL: read (Bio.motifs)
Doctest: Bio.motifs.read
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Traceback (most recent call last):
File "/usr/lib/python2.7/doctest.py", line 2201, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.motifs.read
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 86, in read

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File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 94, in Bio.motifs.read
Failed example:
m = motifs.read(open("motifs/SRF.pfm"), "pfm")
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "", line 1, in
m = motifs.read(open("motifs/SRF.pfm"), "pfm")
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 128, in read
motifs = parse(handle, format)
File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 79, in parse
from Bio.motifs import jaspar
ImportError: cannot import name jaspar
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File "/home/pgarland/Hacking/Source/Biology/biopython/build/lib.linux-x86_64-2.7/Bio/motifs/__init__.py", line 95, in Bio.motifs.read
Failed example:
m.consensus
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python2.7/doctest.py", line 1289, in __run
compileflags, 1) in test.globs
File "", line 1, in
m.consensus
NameError: name 'm' is not defined

~Phillip