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RELEASE_NOTES
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RELEASE_NOTES
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ITEP 1.2
This release includes a number of new features and bug fixes.
NEW FEATURES:
- Beginnings of a crude GUI for common analysis workflows. Currently supported:
- Getting basic information about a gene
- Finding related genes and building crude alignments and trees
- Getting gene neighborhoods and overlaying on the tree
- Getting basic information about related genes
- Getting BLAST support for a gene family.
Note you must have already built the database before running the GUI. Using the gui requires you to have
access to an X11 server and the easygui Python package. It should be considered highly experimental / breakable
at this point.
- OrthoMCL wrapper now takes as input an arbitrary table of BLAST results from the ITEP database
- makeCoreClusterAnalysisTree.py now optionally can be used to analyze presence-absence patterns relative to sister clades,
rather than relative to all organisms in the cluster run. See help text for details.
- db_makeClusterComparisonTable.py - identify genes in the same cluster as a reference across cluster runs and provide
a table in a suitable format for displaying with db_displayTree.py
- db_getEquivalentGenesInOrganism.py - Given a list of query genes, a run ID and an organism, finds all genes in the provided organism that are in the
same cluster as the query genes and returns a conversion table.
- Make a diagram of neighbors for a single gene
BUG FIXES:
- Check for biopython version no longer fails due to letters in the version number. Thanks to Matt Richards for reporting.
- Fix handling of version numbers when number provided in convertGenbankToTable does not match the number in the provided Genbank file.
Thanks to Matt Richards for reporting.
- Fixed handling of sanitized gene IDs (e.g. fig_83333_1_peg_1 intead of fig|83333.1.peg.1) when displaying trees
- Fixed handling of tBLASTn IDs when building gene neighborhood trees
- Fixed coloring of neighborhood trees when cluster cutoff is specified on the command line
- Improved fallback of getGeneNeighborhoods when gene is not found in the specified cluster run. Fallback is now to use cluster ID = -1,
same as it is in the neighborhood display script.
- Fixed replaceGeneNamesWithAliases.py to work with much more general filetypes.
- Improved displaying of labels on neighborhood graphs. Should be much nicer now, no overlapping labels or labels cut off the edge of the image.
- Presence-absence tables no longer print out columns with all NONE (e.g. columns for organisms not found in the specified cluster run).
- Made SourceMe.sh more robust to spaces in the current PATH definition. Thanks to drjcthrash for the inspiration.
- Improved performance of run ID listing and organism links.
- Fixed bug in definition of distinctorgs view (and turned it into a table).
VIRTUAL MACHINE FIXES:
- Added FastTreeMP to virtual machines
- Added easygui to virtual machines
- Upgraded Biopython to 1.63 on both machines
OTHER CHANGES:
- unsanitizeGeneId() function moved to sanitizeString.py library to avoid importing many tree-related libraries when not necessary.
- Several additional script functions have been added to the callable libraries (especially several needed for the UI)
------------------------------
ITEP 1.1: Initial public release.