etal (Eric Talevich)

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Name: Eric Talevich

Email

Website/Blog: http://etalog.blogspot.com/

Location: Athens, GA

Member Since: Feb 07, 2009 (10 months)

Following 4 githubbers and watching 5 repositories view all →

Public Repositories (1)

- 5
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biopython

Eric's personal Biopython branch

Forked from biopython/biopython Sun Mar 15 16:39:25 -0700 2009

Last updated Tue Dec 08 13:49:45 -0800 2009

Public Activity

etal pushed to master at etal/biopython Tue Dec 08 13:49:58 -0800 2009

HEAD is f3e58fe6003a5ccecc1427638e61c5c4b5cc7775

171 commits »

peterjc committed bccc1c78:

Remove the Martel files (they are still there in the history), which were last included in Biopython 1.50 but not installed for 1.51 or 1.52
peterjc committed 0c625208:

Removing Bio.distance (deprecated in Biopython 1.49)
peterjc committed 69f1dcc9:

Updated DEPRECATED file to reflect final name of Bio.SeqIO.index() function
peterjc committed 3972bd6b:

Removing Bio.Ndb (deprecated a year ago in Biopython 1.49)
peterjc committed 7b2a1a51:

Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc committed b8dd8c54:

Merge branch 'master' of git@github.com:biopython/biopython
peterjc committed 0fc67759:

Writing CONTIG line in GenBank output with SeqIO (Bug 2745)
peterjc committed bf7104ee:

Tweak the test suite to ensure keyboard interupts work again (after earlier Jython specific hack)
peterjc committed 53af769d:

Fixed a typo in the tutorial
peterjc committed 82df78f8:

Parse GenBank CONTIG data as a string (like BioPerl which helps with BioSQL compatibility), avoiding problems with elements like gap(unk100). Resolves Bug 2745
peterjc committed 5b119dc4:

Make display order explicit so that test_Nexus.py passes on Jython, fix from Kyle Ellrott posted on github
peterjc committed 51ac4b1a:

test_SubsMat.py should cope when NumPy isn't installed
peterjc committed 762da7e9:

Skip test_trie.py and test_triefind.py on Jython as Bio.trie needs compiled C code
peterjc committed 5556b95d:

Tiny change to how we check for muscle to avoid hanging on Jython under Mac OS X. May indicate a bug in Jython 2.5.0's commants.getoutput() function?
peterjc committed 31ca5797:

Sorting and reduction of decimal places in output to get test_ProtParam.py to pass on both CPython 2.5.2 and Jython 2.5.0
peterjc committed c89e1633:

Sorting in test_seq.py so it works on Jython 2.5.0
peterjc committed 973101b0:

Update run_tests.py to cope with Jython 2.5.0 java.lang.ClassFormatError (which isn't a Python exception) and continue with the test suite (instead of aborting).
peterjc committed 23563ff1:

Sort formats to make sure AlignIO unit test also passes on Jython 2.5.0
peterjc committed ff565fe0:

Dict's iteritems() order different in Jython, fix for Bug 2894 (see also 2887). Tested on Jython 2.5.0
peterjc committed 2d6e9169:

Fix for unknown modified amino acids in PDB polypeptide builder, and adding PYX as a known modified cysteine (Bug 2910)

And 151 more commits...

etal pushed to phyloxml at etal/biopython Tue Dec 08 13:49:46 -0800 2009

HEAD is d48a26aa97a958fc64d675498bba2b9f6f0c5952

etal committed d48a26aa:

Tree: renamed Subtree.label to Subtree.name

etal pushed to phyloxml at etal/biopython Mon Dec 07 12:37:13 -0800 2009

HEAD is d28f5e312e5956a311bde781a3f654e8535e0be3

5 commits »

etal pushed to phyloxml at etal/biopython Fri Nov 20 12:54:33 -0800 2009

HEAD is b3d643e140144f913c830e1cd8dc1611477aafbe

176 commits »

peterjc committed bccc1c78:

Remove the Martel files (they are still there in the history), which were last included in Biopython 1.50 but not installed for 1.51 or 1.52
peterjc committed 0c625208:

Removing Bio.distance (deprecated in Biopython 1.49)
peterjc committed 69f1dcc9:

Updated DEPRECATED file to reflect final name of Bio.SeqIO.index() function
peterjc committed 3972bd6b:

Removing Bio.Ndb (deprecated a year ago in Biopython 1.49)
peterjc committed 7b2a1a51:

Deprecating Bio.Enzyme and Bio.Prosite (use Bio.ExPASy instead)
peterjc committed b8dd8c54:

Merge branch 'master' of git@github.com:biopython/biopython
peterjc committed 0fc67759:

Writing CONTIG line in GenBank output with SeqIO (Bug 2745)
peterjc committed bf7104ee:

Tweak the test suite to ensure keyboard interupts work again (after earlier Jython specific hack)
peterjc committed 53af769d:

Fixed a typo in the tutorial
peterjc committed 82df78f8:

Parse GenBank CONTIG data as a string (like BioPerl which helps with BioSQL compatibility), avoiding problems with elements like gap(unk100). Resolves Bug 2745
peterjc committed 5b119dc4:

Make display order explicit so that test_Nexus.py passes on Jython, fix from Kyle Ellrott posted on github
peterjc committed 51ac4b1a:

test_SubsMat.py should cope when NumPy isn't installed
peterjc committed 762da7e9:

Skip test_trie.py and test_triefind.py on Jython as Bio.trie needs compiled C code
peterjc committed 5556b95d:

Tiny change to how we check for muscle to avoid hanging on Jython under Mac OS X. May indicate a bug in Jython 2.5.0's commants.getoutput() function?
peterjc committed 31ca5797:

Sorting and reduction of decimal places in output to get test_ProtParam.py to pass on both CPython 2.5.2 and Jython 2.5.0
peterjc committed c89e1633:

Sorting in test_seq.py so it works on Jython 2.5.0
peterjc committed 973101b0:

Update run_tests.py to cope with Jython 2.5.0 java.lang.ClassFormatError (which isn't a Python exception) and continue with the test suite (instead of aborting).
peterjc committed 23563ff1:

Sort formats to make sure AlignIO unit test also passes on Jython 2.5.0
peterjc committed ff565fe0:

Dict's iteritems() order different in Jython, fix for Bug 2894 (see also 2887). Tested on Jython 2.5.0
peterjc committed 2d6e9169:

Fix for unknown modified amino acids in PDB polypeptide builder, and adding PYX as a known modified cysteine (Bug 2910)