Activity for SIAM
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José María Fernández committed [r205]
Bumped to version 1.3.3
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Added flag to skip uniprot_trembl processing
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Trying to catch the cause of an exception
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Added generation of graphics (PDF, SVG) from th...
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Found and (hopefully) fixed ancient bug which a...
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Written parser for HMMPfam and HMMScan, and fix...
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Deprecating an unused function
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Lots of code refactoring, so SIAM can work with...
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Several fixes on AC and GAF parsers
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Removing debug traces from code
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After fixing so many incompatibilities between ...
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Lots of fixes towards python 3.3 (but it still ...
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Removing mod_file, and adding several additiona...
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itemgetter/attrgetter fixes
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map objects are iterable, but not subscriptable
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Replacement of file() constructors (removed fro...
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Popen returns binary objects which must be deco...
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Fixed management of the decompression in Python 3
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Better stacktrace reporting
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Fixed exception chaining
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Removed has_key usage on dict-like objects, as ...
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HUGE commit containing the code refactoring nee...
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Exceptions and lambda expressions fixes
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Fixed tabs
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Fixed exception creation, according to python3 ...
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Fixed lambda expressions and exception raising,...
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Fixed lambda expressions for python3
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Fixed tabs and lambda according to python3 stan...
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Really fixed lambda functions
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Tab mangling
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Lambda expressions don't use parentheses
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Tabs
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Python 3.3 does not understand '<>' operator
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installer being prepared for a multi-python env...
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Fixed inconsistent tabulator usage
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Added pythonver infix to SIAM-WS.env file, so b...
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Adding PYTHONVER to the generated variables file
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Compatiblity with python 2.7 and python 3.3
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Due all the compatibility changes applied, it i...
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SIAM needs at least six 1.5.0 in order to have ...
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Adding six compatibility layer for cPickle
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Removed unused module
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More code refactoring: urllib + urllib2 calls t...
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Removing duplicated urllib loading
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Removing more unneeded urllib calls
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Removing unused urllib library
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Second batch of changes, substituting print cal...
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First steps towards having SIAM running both on...
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Call pygraphviz instead of explicitly run "dot"
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Small fixes on graph generation
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Almost all the dependencies, but pygraphviz, ca...
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Improved matrix drawing. It is not perfect, but...
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Fixed obscure corner case related to lost GOA s...
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Forgot insert sentences were stored in class va...
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Python does not understand unary increment/decr...
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Even more insertion improvements
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More tweaks to increase the insertion performance
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Trying to get a performance boost on UniProt in...
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Removing last semi-colon, which was leading to ...
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Fixed extraction of taxonomic identifiers, as i...
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Queries optimized for SQLite
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Optimizations (1 of 2)
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Performance improvements due explicit index cre...
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Typo in method name used to fill in uniprot object
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Lambda functions in Python are not so smart as ...
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Class variables are not reachable in this way f...
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Forgot a parentheses
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Optimization of offline UniProt queries
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Issuing wrong query to the database
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Replacing wrong uses of issubclass by right isi...
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Some code reordering
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[bugfix]Avoided an upstream bug in Python gzip ...
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[feature]OBO parser did not know how to handle ...
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Documenting the program only understands OBO 1.0
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* As some old GOA files were double recompresse...
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Latest versions of setuptools do not have Libra...
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Added UniProxy concept, so we can switch betwee...
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Reworked calls, due the changes in mod_db.SIAMDB
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* Added ID alias table
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Removing unused parameters being passed to the ...
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We cannot discard obsolete terms because they c...
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Documenting new parameter (to be implemented)
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[bugfix] Forgot to store the ec2go_table in the...
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[optimize] As EC list associated to a UniProt e...
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[bugfix] SQLite3 executemany cannot be used wit...
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[bugfix] There could be some corner cases where...
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[bugfix] New code was not assigning the scores ...
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[feature] As new evidence code scores are confi...
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[bugfix] More cosmetic changes
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[bugfix] Cosmetic fixes on the output
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[bugfix] XML Schema was not in sync with genera...
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[bugfix] Another "variable" moved to a class va...
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[bugfix] Sequence_Table was being printed twice!
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[feature] Evidence code scoring system has been...
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[feature] Added new mod_db class, which manages...
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[feature] Added future parameters and descripti...
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[bugfix] On custom GOA gaf file, wrong initiali...
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[bugfix] Make R less dependent on the configura...
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[janitor] Labelling a couple of methods as depr...
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[bugfix] KMlocalHybrid and KMlocalEZHybrid did ...