Add full inference test and remove mutation model ignore_ualabel call (…

…#97)

* Add full inference test and fix mut model ualabel call

* add criteria combinations to smalltest

* fix abundance filepath

Makefile

@@ -5,6 +5,7 @@ install:
 	pip install -e .
 
 test:
+	bash tests/smalltest.sh
 	pytest
 	gctree test
 

gctree/mutation_model.py

@@ -428,11 +428,11 @@ def _mutability_dagfuncs(
     mutation_model = MutationModel(*args, **kwargs)
     dist = _mutability_distance(mutation_model, splits=splits)
 
-    @hdag.utils.access_field("label")
-    @hdag.utils.ignore_ualabel(0)
-    @hdag.utils.access_field("sequence")
-    def distance(seq1, seq2):
-        return dist(seq1, seq2)
+    def distance(node1, node2):
+        if node1.is_root():
+            return 0
+        else:
+            return dist(node1.label.sequence, node2.label.sequence)
 
     return hdag.utils.AddFuncDict(
         {"start_func": lambda n: 0, "edge_weight_func": distance, "accum_func": sum},

tests/idmap.txt

@@ -0,0 +1,43 @@
+GL,
+seq1,VIBM1S4A05
+seq2,VIBM1S4A06
+seq3,VIBM1S4A09
+seq4,VIBM1S4B02
+seq5,VIBM1S4B03
+seq6,VIBM1S4B04
+seq7,VIBM1S4B06
+seq8,VIBM1S4B09
+seq9,VIBM1S4B10:VIBM1S4C09:VIBM1S4H12
+seq10,VIBM1S4B12
+seq11,VIBM1S4C03
+seq12,VIBM1S4C04
+seq13,VIBM1S4C05
+seq14,VIBM1S4C07:VIBM1S4E04:VIBM1S4F07
+seq15,VIBM1S4C08:VIBM1S4F04:VIBM1S4F05
+seq16,VIBM1S4C11
+seq17,VIBM1S4D02
+seq18,VIBM1S4D04
+seq19,VIBM1S4D05
+seq20,VIBM1S4D06
+seq21,VIBM1S4D07
+seq22,VIBM1S4D08
+seq23,VIBM1S4D09
+seq24,VIBM1S4D10
+seq25,VIBM1S4D11
+seq26,VIBM1S4D12
+seq27,VIBM1S4E02
+seq28,VIBM1S4E03
+seq29,VIBM1S4E05:VIBM1S4F02
+seq30,VIBM1S4E06
+seq31,VIBM1S4E08
+seq32,VIBM1S4E09
+seq33,VIBM1S4E12
+seq34,VIBM1S4F09
+seq35,VIBM1S4F10
+seq36,VIBM1S4F11
+seq37,VIBM1S4G03
+seq38,VIBM1S4G04
+seq39,VIBM1S4H07
+seq40,VIBM1S4H08
+seq41,VIBM1S4H09
+seq42,VIBM1S4HHH:VIBM1S4HHJ:VIBM1S4HHK:VIBM1S4HHL:VIBM1S4HHM:VIBM1S4HHA:VIBM1S4HHB:VIBM1S4HHC:VIBM1S4HHD:VIBM1S4HKH:VIBM1S4HLJ:VIBM1S4HMJ:VIBM1S4HAJ:VIBM1S4HBJ:VIBM1S4HKJ:VIBM1S4HDJ:VIBM1S4HCJ

tests/isotypemap.txt

@@ -0,0 +1,65 @@
+VIBM1S4A05, IgG2
+VIBM1S4A06, IgG2
+VIBM1S4A09, IgG2
+VIBM1S4B02, IgG2
+VIBM1S4B03, IgG2
+VIBM1S4B04, IgG2
+VIBM1S4B06, IgG2
+VIBM1S4B09, IgG2
+VIBM1S4B10, IgG2
+VIBM1S4C09, IgG2
+VIBM1S4H12, IgG2
+VIBM1S4B12, IgG2
+VIBM1S4C03, IgG2
+VIBM1S4C04, IgA
+VIBM1S4C05, IgG2
+VIBM1S4C07, IgG2
+VIBM1S4E04, IgG2
+VIBM1S4F07, IgG2
+VIBM1S4C08, IgG2
+VIBM1S4F04, IgG2
+VIBM1S4F05, IgG2
+VIBM1S4C11, IgG2
+VIBM1S4D02, IgG2
+VIBM1S4D04, IgG3
+VIBM1S4D05, IgG2
+VIBM1S4D06, IgA
+VIBM1S4D07, IgG2
+VIBM1S4D08, IgG2
+VIBM1S4D09, IgG2
+VIBM1S4D10, IgG2
+VIBM1S4D11, IgG2
+VIBM1S4D12, IgG2
+VIBM1S4E02, IgG2
+VIBM1S4E03, IgG2
+VIBM1S4E05, IgG2
+VIBM1S4F02, IgG2
+VIBM1S4E06, IgG2
+VIBM1S4E08, IgG2
+VIBM1S4E09, IgG2
+VIBM1S4E12, IgG2
+VIBM1S4F09, IgG2
+VIBM1S4F10, IgG2
+VIBM1S4F11, IgG2
+VIBM1S4G03, IgE
+VIBM1S4G04, IgG2
+VIBM1S4H07, IgG2
+VIBM1S4H08, IgG2
+VIBM1S4H09, IgG2
+VIBM1S4HHH, IgG2
+VIBM1S4HHJ, IgE
+VIBM1S4HHK, IgE
+VIBM1S4HHL, IgE
+VIBM1S4HHM, IgE
+VIBM1S4HHA, IgE
+VIBM1S4HHB, IgE
+VIBM1S4HHC, IgG3
+VIBM1S4HHD, IgG3
+VIBM1S4HKH, IgG3
+VIBM1S4HLJ, IgG3
+VIBM1S4HMJ, IgG3
+VIBM1S4HAJ, IgG3
+VIBM1S4HBJ, IgG3
+VIBM1S4HKJ, IgG3
+VIBM1S4HDJ, IgG3
+VIBM1S4HCJ, IgG3

tests/smalltest.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+export QT_QPA_PLATFORM=offscreen
+export XDG_RUNTIME_DIR=/tmp/runtime-runner
+export MPLBACKEND=agg
+gctree infer tests/small_outfile tests/abundances.csv --root GL --frame 1 --verbose --idlabel 
+gctree infer tests/small_outfile tests/abundances.csv --root GL --frame 1 --verbose --idlabel --idmapfile tests/idmap.txt --isotype_mapfile tests/isotypemap.txt
+gctree infer tests/small_outfile tests/abundances.csv --root GL --frame 1 --verbose --idlabel --mutability S5F/Mutability.csv --substitution S5F/Substitution.csv
+gctree infer tests/small_outfile tests/abundances.csv --root GL --frame 1 --verbose --idlabel --idmapfile tests/idmap.txt --isotype_mapfile tests/isotypemap.txt --mutability S5F/Mutability.csv --substitution S5F/Substitution.csv