kb_phylgenomics 1.4.0

A KBase module for comparative and phylogenomic visualization analysis

What's Changed

• Added unit test for run_DomainAnnotation_Sets by @jmchandonia in #1
• Fixed local call to GeneDomains client by @jmchandonia in #2
• Support for auth2 by @rsutormin in #3
• adding unit tests by @dcchivian in #4
• playing with scaling for pan_circle_plot() by @dcchivian in #5
• playing with scaling for pan_circle_plot() by @dcchivian in #6
• playing with scaling for pan_circle_plot() by @dcchivian in #7
• playing with scaling for pan_circle_plot() by @dcchivian in #8
• playing with scaling for pan_circle_plot() by @dcchivian in #9
• playing with scaling for pan_circle_plot() by @dcchivian in #10
• playing with scaling for pan_circle_plot() by @dcchivian in #11
• playing with pan_circle_plot() scaling by @dcchivian in #12
• playing with scaling for pan_circle_plot() by @dcchivian in #13
• playing with scaling for pan_circle_plot() by @dcchivian in #14
• scaling by @dcchivian in #15
• scaling by @dcchivian in #16
• fix pg_obj name to use actual object name instead of internally store… by @dcchivian in #17
• playing with scaling for pan_circle_plot() by @dcchivian in #18
• playing with scaling for pan_circle_plot() by @dcchivian in #19
• scaling by @dcchivian in #20
• reverse rings to put base genome on outside by @dcchivian in #21
• playing with scaling for pan_circle_plot() by @dcchivian in #22
• playing with scaling for pan_circle_plot() by @dcchivian in #23
• playing with scaling for pan_circle_plot() by @dcchivian in #24
• playing with scaling for pan_circle_plot() by @dcchivian in #25
• scaling by @dcchivian in #26
• playing with scaling for pan_circle_plot() by @dcchivian in #27
• playing with scaling for pan_circle_plot() by @dcchivian in #28
• playing with scaling for pan_circle_plot() by @dcchivian in #29
• playing with scaling for pan_circle_plot() by @dcchivian in #30
• playing with scaling for pan_circle_plot() by @dcchivian in #31
• playing with scaling for pan_circle_plot() by @dcchivian in #32
• playing with scaling for pan_circle_plot() by @dcchivian in #33
• playing with scaling for pan_circle_plot() by @dcchivian in #34
• playing with scaling for pan_circle_plot() by @dcchivian in #35
• playing with scaling for pan_circle_plot() by @dcchivian in #36
• playing with scaling for pan_circle_plot() by @dcchivian in #37
• think I'm done playing with scaling for pan_circle_plot() by @dcchivian in #38
• fix space in obj name by @dcchivian in #39
• remove featureSet element delimiter by @dcchivian in #40
• FeatureSet ids fixed (addresses PUBLIC-215) by @dcchivian in #41
• bumped version to 1.0.1 for view_pan_circle_plot() by @dcchivian in #42
• adding view_tree() by @dcchivian in #43
• bumped versions by @dcchivian in #44
• link App to correct method by @dcchivian in #45
• debugging newick_buf by @dcchivian in #46
• just get rid of problematic (kb|g.1234) part of labels by @dcchivian in #47
• debugging by @dcchivian in #48
• debugging by @dcchivian in #49
• debugging by @dcchivian in #50
• debugging by @dcchivian in #51
• remove debugging by @dcchivian in #52
• make parens brackets instead of hex escape by @dcchivian in #53
• workflow thumbnails by @dcchivian in #54
• resize thumbnails by @dcchivian in #55
• save featuresets from pangenome dissection in view_pan_phylo() by @dcchivian in #56
• tidy up by @dcchivian in #57
• fixing node ids in view_pan_phylo() by @dcchivian in #58
• fix all instances of keys().sort() by @dcchivian in #59
• fixed pangenome obj name setting in view_pan_phylo() by @dcchivian in #60
• typo by @dcchivian in #61
• add logging to debug by @dcchivian in #62
• fix sort of node_num_ids in view_pan_phylo() by @dcchivian in #63
• Fixes for kbReports by @JamesJeffryes in #64
• Highlight user genome in species tree by @JamesJeffryes in #65
• Bump version and revert test changes by @JamesJeffryes in #66
• fix for PTV-1133 / PUBLIC-491 (read 'functions' field in features for Genome-9.0) by @dcchivian in #67
• update version for input widgets by @dcchivian in #68
• fixed version for View_Tree() by @dcchivian in #69
• updated citations and patch by @mclark58 in #71
• Citations for Annotate Domains in a GenomeSet by @mclark58 in #72
• Adding KBase Publication to display.yaml by @thebenallen in #70
• adding find_homologs_with_genome_context() method. dev version 1 by @dcchivian in #73
• debugging by @dcchivian in #74
• fixing table structure and tree row order by @dcchivian in #75
• get leaf ids before replaced by labels by @dcchivian in #76
• typo-level bug by @dcchivian in #77
• getting punchy and making stupid mistakes by @dcchivian in #78
• adjust height of tree and add bait gene header row by @dcchivian in #79
• playing with tree height scaling by @dcchivian in #80
• more playing with tree height scaling by @dcchivian in #81
• rescaling tree by @dcchivian in #82
• fixed typo and more tweaks by @dcchivian in #83
• fixed typo, adding spacing to hit table by @dcchivian in #84
• restored missing var by @dcchivian in #85
• playing with table by @dcchivian in #86
• fix misining key by @dcchivian in #87
• getting punchy by @dcchivian in #88
• playing with tree image by @dcchivian in #89
• trying to fix species tree in html report by @dcchivian in #90
• debugging by @dcchivian in #91
• adding neighbor_thresh option (inactive so far) and fixing genomeSet_ref by @dcchivian in #92
• missing curl by @dcchivian in #93
• need to cast to string by @dcchivian in #94
• debugging by @dcchivian in #95
• adding logic to order features by @dcchivian in #96
• typo by @dcchivian in #97
• typo by @dcchivian in #98
• feature location is a list by @dcchivian in #99
• fixing data names by @dcchivian in #100
• debugging by @dcchivian in #101
• debugging and adding html colors by @dcchivian in #102
• removing leaves by @dcchivian in #103
• playing with vertical scaling by @dcchivian in #104
• playing with vertical scaling by @dcchivian in #105
• playing with vertical scaling by @dcchivian in #106
• playing with vertical scaling by @dcchivian in #107
• playing with vertical scaling by @dcchivian in #108
• playing with color by @dcchivian in #109
• debugging by @dcchivian in #110
• debugging by @dcchivian in #111
• cleaning up table alignment by @dcchivian in #112
• beautification by @dcchivian in #113
• reduced colors by @dcchivian in #114
• explicit cast to int of even number division by @dcchivian in #115
• playing with table spacing by @dcchivian in #116
• playing with table spacing by @dcchivian in #117
• hyperlink genome to genome landing page by @dcchivian in #118
• changed name of html report by @dcchivian in #119
• removed some more lighter colors by @dcchivian in #120
• fixing spacing of tree against genome hit rows by @dcchivian in #121
• adding color_seed field and still working on table row spacing by @dcchivian in #122
• ugh. more vert scaling by @dcchivian in #123
• playing with borders and scaling by @dcchivian in #124
• turned off extra borders by @dcchivian in #125
• still working on spacing by @dcchivian in #126
• beautification by @dcchivian in #127
• fixing bordered cells by @dcchivian in #128
• added cluster color by @dcchivian in #129
• added per genome featureset creation and fixed some bugs by @dcchivian in #130
• typo by @dcchivian in #131
• changing fontsize by @dcchivian in #132
• debugging by @dcchivian in #133
• debugging by @dcchivian in #134
• debugging by @dcchivian in #135
• debugging by @dcchivian in #136
• stop position is really gene length by @dcchivian in #137
• fix last index error on _get_dark_pretty_html_colors() and add cluste… by @dcchivian in #138
• patched SDK_LOCAL client libs by @dcchivian in #139
• make branch_vertical_margin scaled by N_genomes by @dcchivian in #140
• playing more with vertical scaling by @dcchivian in #141
• playing more with vertical scaling by @dcchivian in #142
• playing more with vertical scaling by @dcchivian in #143
• playing more with vertical scaling by @dcchivian in #144
• playing more with vertical scaling by @dcchivian in #145
• typo by @dcchivian in #146
• playing with scaling by @dcchivian in #147
• playing with scaling and tidying headers by @dcchivian in #148
• playing with scaling by @dcchivian in #149
• add blank rows to non-hit cells by @dcchivian in #150
• Change configure categories into separate function by @landml in #151
• Prevent division by zero if no domains found - PTV-1196 by @landml in #152
• Batch 4 Updates by @mclark58 in #153
• app doc round 2 by @mclark58 in #154
• added flexibility to methods that require matching genomes by @dcchivian in #155
• homolog genome context was accidentally released. hiding and will re… by @dcchivian in #156
• tidying logic on skip by @dcchivian in #157
• added logic to permit no DomainAnnotation object if all SEED custom d… by @dcchivian in #158
• fix div by zero for single hit gene by @dcchivian in #159
• added SEED-only logic to VFP FeatureSets and VFP Phylo by @dcchivian in #160
• warn if all genomes have no matching domain annotations by @dcchivian in #161
• fixed logic for SEED only queries by @dcchivian in #162
• move prune before display adjustments and send prune() method retain … by @dcchivian in #163
• added debugging statements by @dcchivian in #164
• more debugging statements by @dcchivian in #165
• fixing debugging statements by @dcchivian in #166
• syntax error by @dcchivian in #167
• genome_refs list already had missing genomes removed by @dcchivian in #168
• syntax error by @dcchivian in #169
• add a blank row to fix alignment of tree to rows by @dcchivian in #170
• save FeatureSet for custom target fam queries by @dcchivian in #171
• saving featureset for custom target fams for view_fxn_profile_phylo() by @dcchivian in #172
• gene_name needs defining in view_fxn_profile_featureset() by @dcchivian in #173
• save domfam slices as featuresets for view_fxn_profile_featuresets() by @dcchivian in #174
• validate SEED subsys vocab for view_fxn_profile_phylo() by @dcchivian in #175
• debugging SEED validation by @dcchivian in #176
• debugging SEED validation by @dcchivian in #177
• more tweaks by @dcchivian in #178
• require 3 or more genomes to draw tree in vfp_phylo() by @dcchivian in #179
• add validation of annotations, fraction covered, etc. by @dcchivian in #180
• allow SpeciesTree as input to run_DomainAnnotation_Sets() by @dcchivian in #181
• tidied up drop down options for TIGR and SEED for PTV-1294 by @dcchivian in #182
• added display_genome_object_name option to VFP Apps to fix ticket PTV… by @dcchivian in #183
• got some bugs out by @dcchivian in #184
• added user control of fraction annotated within each namespace by @dcchivian in #185
• fraction_requiring_annotation variable was outside namespace loop by @dcchivian in #186
• vertical must be passed in unittest since value not derived from spec… by @dcchivian in #187
• added option to display genome sci name, obj name, and version. made… by @dcchivian in #188
• restore all unit tests by @dcchivian in #189
• added new options to VFP apps by @dcchivian in #190
• got the bugs out by @dcchivian in #191
• got more bugs out. sorting genome display names and requiring unique… by @dcchivian in #192
• combined 3 display_genome options into a single parameter genome_disp… by @dcchivian in #193
• added trim_speciestree_to_genomeset() App by @dcchivian in #194
• tidying and improving defaults and messaging for VFP apps by @dcchivian in #195
• tweaked messages and defaults to respond to PTV-1287 and PTV-1289 by @dcchivian in #196
• tidying up, including updating App Docs to match VFP options by @dcchivian in #197
• added screenshots to App Docs for VFP by @dcchivian in #198

New Contributors

• @rsutormin made their first contribution in #3
• @JamesJeffryes made their first contribution in #64
• @mclark58 made their first contribution in #71
• @thebenallen made their first contribution in #70
• @landml made their first contribution in #151

Full Changelog: https://github.com/kbaseapps/kb_phylogenomics/commits/1.4.0