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Experimental ui#68

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ghost wants to merge 26 commits intomasterfrom

Commits on May 28, 2014

Update UI base and add some experimental UI functions
Matthew Benedict
committed
Commit experimental UI function
Matthew Benedict
committed
Commit experimental UI function
Matthew Benedict
committed

Commits on May 29, 2014

Fix bug in saving files...
Matthew Benedict
committed
Remove errant print statement
Matthew Benedict
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Update makeCoreClusterAnalysisTree - allow use of trees with organism IDs instead of names to make it more consistent with other tree accepting programs
Matthew Benedict
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Update release notes
Matthew Benedict
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Incremental improvement to tree UI
Matthew Benedict
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Bugfix
Matthew Benedict
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Add a useful script to find the ortholog of a gene in a particular organism
Matthew Benedict
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Make output file a required argument to several scripts. It reduces confusion about where things end up
Matthew Benedict
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Improve temp file handling in tblastn wrapper
Matthew Benedict
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Add index for organism ID in contig table - useful for tblastn wrapper
Matthew Benedict
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Remove unnecessary import
Matthew Benedict
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Commits on May 30, 2014

Adding headers
Matthew Benedict
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Fix bug in SingleGeneAnalysis
Matthew Benedict
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Check for xlwt (needed for excel export in one script)
Matthew Benedict
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More headers. About halfway done?
Matthew Benedict
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Improve more help text and fix db_makeClusterComparisonTable.py. The latter now distinguishes between cases in which an organism is not included in a cluster run and those in which it is but the ge…
Matthew Benedict
committed
Improve help text
Matthew Benedict
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Fix bug in db_makeNeighborhoodTree.py
Matthew Benedict
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Remove errant comment
Matthew Benedict
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Commits on May 31, 2014

Default orthomcl file name should not be all any more but should depend on the file given as input
Matthew Benedict
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Commits on Jun 3, 2014

Make locus tag not case sensitive
Matthew Benedict
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Update release notes
Matthew Benedict
committed

Commits on Jul 4, 2014

Improve robustness to strange characters in sequences
Matthew Benedict
committed