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CHANGELOG

Summary

  • Unreleased changes
  • Release 2020-06-23 1.0.3
    • Added code to download background genes from NCBI.
    • Fixed the 'write hierarchy' script, wr_hier.py, so it will write MF and CC hierarchies.
  • Release 2020-03-13 1.0.3 GOEAs can be run in quiet mode
  • Release 2020-02-20 1.0.2
    • Added Jupyter notebook showing how to work with obsolete GO terms #153 #154 #155
    • Deprecated: Internal data member, go2parents will be deprecated, renamed to go2ancestors
  • Release 2019-09-29 0.9.7
    • Deprecated: read_ncbi_gene2go
    • Deprecated: get_b2aset and GoDagTimed in their old location. They have been moved.
    • Removed empty sets from Descendant and Ancestor dicts in gosubdag.rcntobj
    • TermCount improvements (used in semantic similarity calculations)
    • GO DAG Plotting:
      • User can now add a title to GO DAG plots
      • User can now add custom text to edges in GO DAG plots
  • Release 2019-07-26 0.9.7
    • Support user-specified optional relationships in GOEA propagate counts
  • Release 2019-05-08 0.9.5
    • Support user-specified evidence codes in GOEAs
    • Separate GOEAs into BP, MF, and CC

Unreleased changes

  • Added
    • Added a script to duplicate Table 2 in the GOATOOLS publication #171
    • Added clear documentation to explain GO term text (D and R) in plots #178

Release 2020-06-23 1.0.6

  • Fixed
    • The scripts/wr_hier.pyi script can now print the hierarchy for GO IDs in all namespaces. #163
    • The semantic_similarity function upon comparing a GO term to itself. #150
  • Added
    • Added a new notebook showing how to download background genes from NCBI.
    • Added arg, --prt_study_gos_only, to script, scripts/find_enrichment.py to print only study GOs when printing all GO terms, regardless of their significance (--pval=1.0):
      find_enrichment.py study_genes.txt human_genes.txt gene2go --pval=1.0 --prt_study_gos_only
  • Changed

Release 2020-03-13 1.0.3

  • Added
    • Added quiet mode when running GOEAs using the function, run_goea. Examples are in section 5a. Quietly Run a GOEA of the GOEA Jupyter notebook. re: See comments (1 and 2) in #133

Release 2020-02-20 1.0.2

  • Added
  • Deprecated
    • Renamed internal data variable:
      • NOW: gosubdag.rcntobj.go2ancestors
      • WAS: gosubdag.rcntobj.go2parents
  • Changed
    • Issue 148 Return None for Lin's semantic similarity calculations if one or both of the GO terms is not annotated. This will be updated in the future to have the option to assign a count of 1 to GO terms that are not annotated, indicating the annotation of a mock gene to allow the researcher to get a rough idea of the similarity.
    • Issue 142
      • Write GO hierachy to a file now writes a file when using Python3
      • Gaf reader defaults to gaf file version of 2.1 if no version line if found

Release 2019-09-29 0.9.9

  • Deprecated
    • read_ncbi_gene2go is deprecated and will be removed in the future.
    • get_b2aset is moved:
      • NOW: goatools.utils
      • WAS: goatools.associations
    • GoDagTimed and prt_hms is moved:
      • NOW: goatools.godag.prttime
      • WAS: goatools.test_data.godag_timed
  • Removed
    • All dict entries whose values were an empty set in:
      • gosubdag.rcntobj.go2parents
      • gosubdag.rcntobj.go2descendants
  • Added`
    • Method to annotation object, IdToGosReader, which writes namedtuples into an ASCII file
  • Changed
    • TermCounts:
      • Added support for optional relationships, like part_of.
        This is useful for computing termwise and genewise semantic similarities.
      • Faster initialization of TermCounts object, used in semantic similarity calculations
    • Plotting:
      • Users can now provide a title to be printed in a GO DAG plot
      • Users can now provide an edge2txt dict to print text on edges between GO Terms
  • Fixed
    • Aspect counts (BP, MF, CC totals) in TermCounts object explained in #156

Release 2019-07-26 0.9.7

Summary

  • Added
    • Support traversing optional relationships when propagating counts for GOEAs

Details

  • Support traversing optional relationships, like part_of and regulates, when doing propagating counts using these two new arguments in scripts/find_enrichment.py:
        -r, --relationship    Propagate counts up all relationships (default: False)
       --relationships        [RELATIONSHIPS [RELATIONSHIPS ...]]
                               Propagate counts up user-specified relationships
                               (default: None)

tanghaibao#117 (comment)

Release 2019-05-08 0.9.5

Summary

Details

Added support for specifying specific evidence codes:

  • Specify evidence codes, like EXP (Inferred from Experiment), to exclude or include in a GOEA.
  • Specify evidence classes, like Experimental (EXP IDA IPI IMP IGI IEP), which include many evidence codes.
  • Get evidence code help:
  $ python3 scripts/find_enrichment.py --ev_help
  $ python3 scripts/find_enrichment.py --ev_help_short

tanghaibao#119 (comment)
tanghaibao#119 (comment)

Added splitting GOEA into BP, MF, and CC

Split GOEA into three separate analyses by default:

  • BP (biological process)
  • MF (molecular function)
  • CC cellular component)

tanghaibao#127 (comment)

Release 2018-11-27 0.8.12

Release 2018-11-21 0.8.11

Release 2018-09-09 0.8.9

Release 2018-04-28 0.8.4

Release 2018-02-22 0.8.2

Release 2018-02-19 0.7.11

Release 2018-01-07 0.7.11

Release 2017-10-14 0.7.11

Release 2017-10-07 0.7.10

Release 2015-02-05

Release 2014-08-10

Release 2010-04-12

Release 2010-02-23

https://keepachangelog.com/en/1.0.0/ git log --since=2019-05-08 --before=2019-07-26