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Fix ImpliedLosses: look up taxonomic levels by name #126

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Merged
alpae merged 1 commit into from
Nov 4, 2026
Merged

Fix ImpliedLosses: look up taxonomic levels by name #126

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13 changes: 9 additions & 4 deletions FastOMA/_hog_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,21 +92,26 @@ def _hog_implied_losses(hog: "HOG", tree_node: TreeNode) -> int:
Mirrors _tax_overlap's _tax_now-based grouping of _subhogs, but sums losses per group member
instead of intersecting/folding lineages: a group of sub-hogs sharing the same _tax_now
represents a duplication, and each such paralogous copy's losses are counted independently
so that one copy's presence in a species can't mask a sibling copy's loss there."""
so that one copy's presence in a species can't mask a sibling copy's loss there.

The sub-hogs' taxonomic levels are looked up by name in `tree_node`'s tree: their `_tax_now`
nodes belong to other tree objects (the pruned working tree, and a separate copy per pickled
level), and ete3 nodes only compare by identity."""
subhogs = getattr(hog, "_subhogs", None)
if not subhogs:
return 0

index = _species_name_index(tree_node)
losses = 0
clade_groups = {}
for sh in subhogs:
clade_groups.setdefault(sh._tax_now.name, []).append(sh)
for subhogs_of_clade in clade_groups.values():
clade_node = subhogs_of_clade[0]._tax_now
for clade_name, subhogs_of_clade in clade_groups.items():
clade_node = index[clade_name]
for sh in subhogs_of_clade:
losses += _hog_implied_losses(sh, clade_node)

reached_nodes = [subhogs_of_clade[0]._tax_now for subhogs_of_clade in clade_groups.values()]
reached_nodes = [index[clade_name] for clade_name in clade_groups]
losses += _count_untouched_clades(tree_node, reached_nodes)
return losses

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10 changes: 5 additions & 5 deletions tests/data/fungi30/golden/F0413304.txt
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@@ -1,10 +1,10 @@
# 4 input proteins, 2 groups, 4 proteins in groups

orthologGroup Fungi CompletenessScore=0.0667 ImpliedLosses=2 TCSScore=0.0
tr|A0A1Y2ETJ6|A0A1Y2ETJ6_9FUNG
tr|A0AA35IW45|A0AA35IW45_SACMI

orthologGroup Fungi CompletenessScore=0.0667 ImpliedLosses=3 TCSScore=0.0
orthologGroup Fungi CompletenessScore=0.0667 ImpliedLosses=5 TCSScore=0.0
paralogGroup
tr|A0A1Y2AI63|A0A1Y2AI63_9FUNG
tr|A0ABQ8PQ38|A0ABQ8PQ38_9FUNG

orthologGroup Fungi CompletenessScore=0.0667 ImpliedLosses=5 TCSScore=0.0
tr|A0A1Y2ETJ6|A0A1Y2ETJ6_9FUNG
tr|A0AA35IW45|A0AA35IW45_SACMI
44 changes: 22 additions & 22 deletions tests/data/fungi30/golden/F0453151.txt
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@@ -1,7 +1,7 @@
# 101 input proteins, 1 groups, 86 proteins in groups

orthologGroup Fungi CompletenessScore=0.6667 ImpliedLosses=120 TCSScore=20.314
orthologGroup Dikarya CompletenessScore=0.6923 ImpliedLosses=118 TCSScore=17.4933
orthologGroup Fungi CompletenessScore=0.6667 ImpliedLosses=114 TCSScore=20.314
orthologGroup Dikarya CompletenessScore=0.6923 ImpliedLosses=112 TCSScore=17.4933
orthologGroup Basidiomycota CompletenessScore=0.375 ImpliedLosses=3 TCSScore=2.2
paralogGroup
orthologGroup Ustilaginomycotina CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.6667
Expand All @@ -12,33 +12,33 @@ orthologGroup Fungi CompletenessScore=0.6667 ImpliedLosses=120 TCSScore=20.314
tr|A0A0F7S400|A0A0F7S400_9BASI
tr|M7XCB9|M7XCB9_RHOT1
paralogGroup
orthologGroup Sordariomycetes CompletenessScore=0.4444 ImpliedLosses=4 TCSScore=1.5
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Sordariomycetes CompletenessScore=0.4444 ImpliedLosses=2 TCSScore=1.5
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A7J6IG66|A0A7J6IG66_COLFN
tr|A0AAX4IHJ5|A0AAX4IHJ5_9PEZI
orthologGroup Sordariomycetidae CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
tr|A0A2P5HUN9|A0A2P5HUN9_DIAHE
tr|A0ABQ8NNB3|A0ABQ8NNB3_PYRGI
orthologGroup leotiomyceta CompletenessScore=0.25 ImpliedLosses=8 TCSScore=4.25
orthologGroup Hypocreales CompletenessScore=0.75 ImpliedLosses=2 TCSScore=0.6667
orthologGroup Hypocreales CompletenessScore=0.75 ImpliedLosses=1 TCSScore=0.6667
orthologGroup Fusarium CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
tr|A0A395SPL0|A0A395SPL0_FUSSP
tr|A0A8H5KVI5|A0A8H5KVI5_GIBSU
tr|G9N0Q0|G9N0Q0_HYPVG
tr|F2PYR0|F2PYR0_TRIEC
orthologGroup leotiomyceta CompletenessScore=0.9375 ImpliedLosses=101 TCSScore=5.0161
orthologGroup leotiomyceta CompletenessScore=0.9375 ImpliedLosses=94 TCSScore=5.0161
paralogGroup
orthologGroup Eurotiomycetes CompletenessScore=1.0 ImpliedLosses=4 TCSScore=2.4
orthologGroup Eurotiomycetidae CompletenessScore=1.0 ImpliedLosses=3 TCSScore=1.0
orthologGroup Aspergillaceae CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Eurotiomycetes CompletenessScore=1.0 ImpliedLosses=0 TCSScore=2.4
orthologGroup Eurotiomycetidae CompletenessScore=1.0 ImpliedLosses=0 TCSScore=1.0
orthologGroup Aspergillaceae CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A1L9VRU9|A0A1L9VRU9_ASPGL
tr|A0A1V6PLF3|A0A1V6PLF3_PENDC
orthologGroup Onygenales CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Onygenales CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A1B7NX54|A0A1B7NX54_9EURO
tr|F2Q0I0|F2Q0I0_TRIEC
tr|A0A0D2FPJ6|A0A0D2FPJ6_CLAB1
paralogGroup
orthologGroup Eurotiomycetidae CompletenessScore=0.75 ImpliedLosses=6 TCSScore=0.8
orthologGroup Eurotiomycetidae CompletenessScore=0.75 ImpliedLosses=5 TCSScore=0.8
paralogGroup
tr|A0A1B7NXM4|A0A1B7NXM4_9EURO
tr|F2PIH5|F2PIH5_TRIEC
Expand All @@ -53,19 +53,19 @@ orthologGroup Fungi CompletenessScore=0.6667 ImpliedLosses=120 TCSScore=20.314
tr|F2PM61|F2PM61_TRIEC
tr|F2PV36|F2PV36_TRIEC
paralogGroup
orthologGroup Fusarium CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Fusarium CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A395S0Z2|A0A395S0Z2_FUSSP
tr|A0A8H5P5V9|A0A8H5P5V9_GIBSU
tr|A0A9P9JQS6|A0A9P9JQS6_FUSSL
orthologGroup Hypocreales CompletenessScore=0.75 ImpliedLosses=2 TCSScore=1.0
orthologGroup Hypocreales CompletenessScore=0.75 ImpliedLosses=1 TCSScore=1.0
orthologGroup Fusarium CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
tr|A0A395SR55|A0A395SR55_FUSSP
tr|A0A8H5PCB0|A0A8H5PCB0_GIBSU
paralogGroup
tr|G9MUQ4|G9MUQ4_HYPVG
tr|G9MZ61|G9MZ61_HYPVG
orthologGroup Hypocreomycetidae CompletenessScore=0.5 ImpliedLosses=4 TCSScore=0.6667
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Hypocreomycetidae CompletenessScore=0.5 ImpliedLosses=3 TCSScore=0.6667
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A7J6ID17|A0A7J6ID17_COLFN
tr|A0AAX4J184|A0AAX4J184_9PEZI
tr|A0A395S871|A0A395S871_FUSSP
Expand All @@ -82,17 +82,17 @@ orthologGroup Fungi CompletenessScore=0.6667 ImpliedLosses=120 TCSScore=20.314
tr|G9MUY2|G9MUY2_HYPVG
tr|G9N4C5|G9N4C5_HYPVG
tr|A0ABQ8NPS7|A0ABQ8NPS7_PYRGI
orthologGroup Sordariomycetes CompletenessScore=0.5556 ImpliedLosses=5 TCSScore=3.4
orthologGroup Hypocreales CompletenessScore=1.0 ImpliedLosses=2 TCSScore=0.75
orthologGroup Fusarium CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Sordariomycetes CompletenessScore=0.5556 ImpliedLosses=3 TCSScore=3.4
orthologGroup Hypocreales CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.75
orthologGroup Fusarium CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A395SQY0|A0A395SQY0_FUSSP
tr|A0A8H5Q5X1|A0A8H5Q5X1_GIBSU
tr|A0A9P9HA30|A0A9P9HA30_FUSSL
tr|G9MWP4|G9MWP4_HYPVG
tr|A0A2P5IFJ7|A0A2P5IFJ7_DIAHE
orthologGroup Sordariomycetes CompletenessScore=0.6667 ImpliedLosses=6 TCSScore=2.3333
orthologGroup Hypocreomycetidae CompletenessScore=0.6667 ImpliedLosses=4 TCSScore=1.0
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Sordariomycetes CompletenessScore=0.6667 ImpliedLosses=3 TCSScore=2.3333
orthologGroup Hypocreomycetidae CompletenessScore=0.6667 ImpliedLosses=2 TCSScore=1.0
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0AAX4IDB4|A0AAX4IDB4_9PEZI
tr|L2FJK3|L2FJK3_COLFN
orthologGroup Hypocreales CompletenessScore=0.5 ImpliedLosses=2 TCSScore=0.0
Expand Down Expand Up @@ -122,7 +122,7 @@ orthologGroup Fungi CompletenessScore=0.6667 ImpliedLosses=120 TCSScore=20.314
paralogGroup
tr|A0A7C8I9Y5|A0A7C8I9Y5_9PLEO
tr|A0A7C8IAS7|A0A7C8IAS7_9PLEO
orthologGroup Fungiincertaesedis CompletenessScore=0.5 ImpliedLosses=1 TCSScore=0.9091
orthologGroup Fungiincertaesedis CompletenessScore=0.5 ImpliedLosses=2 TCSScore=0.9091
paralogGroup
tr|A0A1Y1YU83|A0A1Y1YU83_9FUNG
tr|A0A1Y2A814|A0A1Y2A814_9FUNG
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16 changes: 8 additions & 8 deletions tests/data/fungi30/golden/F0459413.txt
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@@ -1,15 +1,15 @@
# 26 input proteins, 1 groups, 26 proteins in groups

orthologGroup Dikarya CompletenessScore=0.4615 ImpliedLosses=25 TCSScore=20.6538
orthologGroup Basidiomycota CompletenessScore=0.25 ImpliedLosses=1 TCSScore=0.6667
orthologGroup Dikarya CompletenessScore=0.4615 ImpliedLosses=33 TCSScore=20.6538
orthologGroup Basidiomycota CompletenessScore=0.25 ImpliedLosses=4 TCSScore=0.6667
paralogGroup
tr|M7WKC3|M7WKC3_RHOT1
tr|M7XDE6|M7XDE6_RHOT1
tr|A0A067TG69|A0A067TG69_GALM3
paralogGroup
orthologGroup leotiomyceta CompletenessScore=0.4375 ImpliedLosses=7 TCSScore=4.1111
orthologGroup leotiomyceta CompletenessScore=0.4375 ImpliedLosses=9 TCSScore=4.1111
orthologGroup Sordariomycetes CompletenessScore=0.4444 ImpliedLosses=4 TCSScore=4.0
orthologGroup Hypocreales CompletenessScore=0.75 ImpliedLosses=2 TCSScore=1.0
orthologGroup Hypocreales CompletenessScore=0.75 ImpliedLosses=1 TCSScore=1.0
orthologGroup Fusarium CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
tr|A0A8H5NQD1|A0A8H5NQD1_GIBSU
tr|A0A9P9KTM1|A0A9P9KTM1_FUSSL
Expand All @@ -23,16 +23,16 @@ orthologGroup Dikarya CompletenessScore=0.4615 ImpliedLosses=25 TCSScore=20.653
paralogGroup
tr|A0A7C8IAK2|A0A7C8IAK2_9PLEO
tr|A0A7C8MMZ9|A0A7C8MMZ9_9PLEO
orthologGroup leotiomyceta CompletenessScore=0.5625 ImpliedLosses=16 TCSScore=9.5
orthologGroup leotiomyceta CompletenessScore=0.5625 ImpliedLosses=18 TCSScore=9.5
paralogGroup
orthologGroup Sordariomycetes CompletenessScore=0.6667 ImpliedLosses=7 TCSScore=7.3333
orthologGroup Sordariomycetes CompletenessScore=0.6667 ImpliedLosses=6 TCSScore=7.3333
paralogGroup
orthologGroup Hypocreales CompletenessScore=1.0 ImpliedLosses=3 TCSScore=2.2857
orthologGroup Hypocreales CompletenessScore=1.0 ImpliedLosses=1 TCSScore=2.2857
paralogGroup
orthologGroup Fusarium CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
tr|A0A395SGZ3|A0A395SGZ3_FUSSP
tr|A0A9P9KT16|A0A9P9KT16_FUSSL
orthologGroup Fusarium CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.5
orthologGroup Fusarium CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.5
paralogGroup
tr|A0A9P9HBT0|A0A9P9HBT0_FUSSL
tr|A0A9P9KT27|A0A9P9KT27_FUSSL
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14 changes: 7 additions & 7 deletions tests/data/fungi30/golden/F0476910.txt
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
# 34 input proteins, 1 groups, 33 proteins in groups

orthologGroup Fungi CompletenessScore=0.3667 ImpliedLosses=19 TCSScore=12.1515
orthologGroup Fungi CompletenessScore=0.3667 ImpliedLosses=38 TCSScore=12.1515
paralogGroup
orthologGroup Dikarya CompletenessScore=0.3077 ImpliedLosses=7 TCSScore=9.0
orthologGroup leotiomyceta CompletenessScore=0.375 ImpliedLosses=4 TCSScore=1.8571
orthologGroup Sordariomycetes CompletenessScore=0.3333 ImpliedLosses=2 TCSScore=2.0
orthologGroup Dikarya CompletenessScore=0.3077 ImpliedLosses=14 TCSScore=9.0
orthologGroup leotiomyceta CompletenessScore=0.375 ImpliedLosses=6 TCSScore=1.8571
orthologGroup Sordariomycetes CompletenessScore=0.3333 ImpliedLosses=5 TCSScore=2.0
orthologGroup Fusarium CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
tr|A0A395SBE1|A0A395SBE1_FUSSP
tr|A0A9P9R990|A0A9P9R990_FUSSL
Expand Down Expand Up @@ -33,12 +33,12 @@ orthologGroup Fungi CompletenessScore=0.3667 ImpliedLosses=19 TCSScore=12.1515
tr|A0A0C3CHJ8|A0A0C3CHJ8_HEBCY
tr|A0A0C3CIW7|A0A0C3CIW7_HEBCY
tr|A0A067STW1|A0A067STW1_GALM3
orthologGroup leotiomyceta CompletenessScore=0.125 ImpliedLosses=3 TCSScore=0.0
orthologGroup leotiomyceta CompletenessScore=0.125 ImpliedLosses=5 TCSScore=0.0
tr|A0A164Z8X8|A0A164Z8X8_XYLHT
tr|A0A1V6NNK1|A0A1V6NNK1_PENDC
orthologGroup leotiomyceta CompletenessScore=0.25 ImpliedLosses=3 TCSScore=4.2
orthologGroup Eurotiomycetes CompletenessScore=0.6 ImpliedLosses=2 TCSScore=3.0
orthologGroup Aspergillaceae CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.6667
orthologGroup Eurotiomycetes CompletenessScore=0.6 ImpliedLosses=1 TCSScore=3.0
orthologGroup Aspergillaceae CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.6667
paralogGroup
tr|A0A1L9V458|A0A1L9V458_ASPGL
tr|A0A1L9VLC0|A0A1L9VLC0_ASPGL
Expand Down
14 changes: 7 additions & 7 deletions tests/data/fungi30/golden/F0477229.txt
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Original file line number Diff line number Diff line change
@@ -1,30 +1,30 @@
# 27 input proteins, 1 groups, 21 proteins in groups

orthologGroup Dikarya CompletenessScore=0.4615 ImpliedLosses=15 TCSScore=16.0476
orthologGroup Dikarya CompletenessScore=0.4615 ImpliedLosses=17 TCSScore=16.0476
orthologGroup Agaricales CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.6667
paralogGroup
tr|A0A067S4V6|A0A067S4V6_GALM3
tr|A0A067T8Z9|A0A067T8Z9_GALM3
tr|A0A0C3CZU8|A0A0C3CZU8_HEBCY
orthologGroup leotiomyceta CompletenessScore=0.625 ImpliedLosses=13 TCSScore=6.1111
orthologGroup Onygenales CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.75
orthologGroup leotiomyceta CompletenessScore=0.625 ImpliedLosses=11 TCSScore=6.1111
orthologGroup Onygenales CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.75
paralogGroup
tr|F2PXP9|F2PXP9_TRIEC
tr|F2PYJ4|F2PYJ4_TRIEC
tr|F2Q4D0|F2Q4D0_TRIEC
tr|A0A1B7P4W4|A0A1B7P4W4_9EURO
paralogGroup
orthologGroup Sordariomycetes CompletenessScore=0.6667 ImpliedLosses=5 TCSScore=4.1
orthologGroup Hypocreomycetidae CompletenessScore=0.6667 ImpliedLosses=3 TCSScore=2.25
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.8333
orthologGroup Sordariomycetes CompletenessScore=0.6667 ImpliedLosses=3 TCSScore=4.1
orthologGroup Hypocreomycetidae CompletenessScore=0.6667 ImpliedLosses=2 TCSScore=2.25
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.8333
paralogGroup
tr|A0A7J6ICM4|A0A7J6ICM4_COLFN
tr|A0A7J6IHN8|A0A7J6IHN8_COLFN
tr|A0A7J6IMY3|A0A7J6IMY3_COLFN
tr|A0A7J6JBZ8|A0A7J6JBZ8_COLFN
tr|L2GDX0|L2GDX0_COLFN
tr|A0AAX4I0N0|A0AAX4I0N0_9PEZI
orthologGroup Hypocreales CompletenessScore=0.5 ImpliedLosses=1 TCSScore=0.0
orthologGroup Hypocreales CompletenessScore=0.5 ImpliedLosses=2 TCSScore=0.0
tr|A0A9P9JYY1|A0A9P9JYY1_FUSSL
tr|G9MTS0|G9MTS0_HYPVG
orthologGroup Sordariomycetidae CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
Expand Down
4 changes: 2 additions & 2 deletions tests/data/fungi30/golden/F0478382.txt
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@@ -1,7 +1,7 @@
# 4 input proteins, 1 groups, 3 proteins in groups

orthologGroup leotiomyceta CompletenessScore=0.1875 ImpliedLosses=2 TCSScore=1.3333
orthologGroup Hypocreomycetidae CompletenessScore=0.3333 ImpliedLosses=1 TCSScore=0.0
orthologGroup leotiomyceta CompletenessScore=0.1875 ImpliedLosses=7 TCSScore=1.3333
orthologGroup Hypocreomycetidae CompletenessScore=0.3333 ImpliedLosses=4 TCSScore=0.0
tr|A0A8H5V9V0|A0A8H5V9V0_GIBSU
tr|A0AAX4IL06|A0AAX4IL06_9PEZI
tr|A0A7C8ICJ0|A0A7C8ICJ0_9PLEO
18 changes: 9 additions & 9 deletions tests/data/fungi30/golden/F0480898.txt
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@@ -1,8 +1,8 @@
# 24 input proteins, 1 groups, 24 proteins in groups

orthologGroup leotiomyceta CompletenessScore=0.625 ImpliedLosses=21 TCSScore=6.5833
orthologGroup leotiomyceta CompletenessScore=0.625 ImpliedLosses=19 TCSScore=6.5833
paralogGroup
orthologGroup Eurotiomycetidae CompletenessScore=0.5 ImpliedLosses=1 TCSScore=1.5
orthologGroup Eurotiomycetidae CompletenessScore=0.5 ImpliedLosses=2 TCSScore=1.5
paralogGroup
tr|A0A1L9V4W9|A0A1L9V4W9_ASPGL
tr|A0A1L9V7S2|A0A1L9V7S2_ASPGL
Expand All @@ -12,31 +12,31 @@ orthologGroup leotiomyceta CompletenessScore=0.625 ImpliedLosses=21 TCSScore=6.
paralogGroup
orthologGroup Sordariomycetes CompletenessScore=0.3333 ImpliedLosses=7 TCSScore=2.8
paralogGroup
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A7J6JGH0|A0A7J6JGH0_COLFN
tr|A0AAX4I0Q8|A0AAX4I0Q8_9PEZI
tr|L2FWK4|L2FWK4_COLFN
paralogGroup
tr|A0ABQ8NRX1|A0ABQ8NRX1_PYRGI
tr|A0ABQ8NYR1|A0ABQ8NYR1_PYRGI
orthologGroup Sordariomycetes CompletenessScore=0.7778 ImpliedLosses=8 TCSScore=3.9091
orthologGroup Sordariomycetidae CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Sordariomycetes CompletenessScore=0.7778 ImpliedLosses=3 TCSScore=3.9091
orthologGroup Sordariomycetidae CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A2P5I609|A0A2P5I609_DIAHE
tr|A0ABQ8NGB4|A0ABQ8NGB4_PYRGI
tr|V5IKJ7|V5IKJ7_NEUCR
paralogGroup
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0A7J6J4I6|A0A7J6J4I6_COLFN
tr|A0AAX4I0H8|A0AAX4I0H8_9PEZI
orthologGroup Hypocreomycetidae CompletenessScore=0.6667 ImpliedLosses=4 TCSScore=2.0
orthologGroup Hypocreomycetidae CompletenessScore=0.6667 ImpliedLosses=2 TCSScore=2.0
orthologGroup Fusarium CompletenessScore=0.6667 ImpliedLosses=1 TCSScore=0.0
tr|A0A8H5Q8E8|A0A8H5Q8E8_GIBSU
tr|A0A9P9L841|A0A9P9L841_FUSSL
paralogGroup
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0AAX4ICN6|A0AAX4ICN6_9PEZI
tr|L2FCD7|L2FCD7_COLFN
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=1 TCSScore=0.0
orthologGroup Colletotrichum CompletenessScore=1.0 ImpliedLosses=0 TCSScore=0.0
tr|A0AAX4ITE2|A0AAX4ITE2_9PEZI
tr|L2FSM0|L2FSM0_COLFN
tr|A0A7J6J952|A0A7J6J952_COLFN
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6 changes: 3 additions & 3 deletions tests/data/fungi30/golden/F0489906.txt
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Original file line number Diff line number Diff line change
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# 6 input proteins, 1 groups, 6 proteins in groups

orthologGroup Dikarya CompletenessScore=0.1923 ImpliedLosses=5 TCSScore=8.1667
orthologGroup Dikarya CompletenessScore=0.1923 ImpliedLosses=23 TCSScore=8.1667
paralogGroup
orthologGroup leotiomyceta CompletenessScore=0.25 ImpliedLosses=3 TCSScore=1.75
orthologGroup leotiomyceta CompletenessScore=0.25 ImpliedLosses=9 TCSScore=1.75
orthologGroup Eurotiomycetes CompletenessScore=0.6 ImpliedLosses=2 TCSScore=0.6667
orthologGroup Eurotiomycetidae CompletenessScore=0.5 ImpliedLosses=1 TCSScore=0.0
orthologGroup Eurotiomycetidae CompletenessScore=0.5 ImpliedLosses=2 TCSScore=0.0
tr|A0A1B7NPW6|A0A1B7NPW6_9EURO
tr|A0A1L9VKP1|A0A1L9VKP1_ASPGL
tr|A0A0D2ESI3|A0A0D2ESI3_CLAB1
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