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test.sh
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test.sh
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########## Test Suite for Gotree command line tools ##############
set -e
set -u
set -o pipefail
TESTDATA="tests/data"
GOTREE=./gotree
# gotree stats with comments before tree
echo "->gotree stats with []"
cat > input <<EOF
[comment](Tip3,Tip0,((Tip4,Tip2),Tip1));
(Tip4,Tip0,((Tip3,Tip2),Tip1));
[comment;():,](Tip2,Tip0,((Tip4,Tip3),Tip1));
(Tip2,Tip0,((Tip4,Tip3),Tip1));
EOF
cat > expected <<EOF
tips
5
5
5
5
EOF
${GOTREE} stats -i input | cut -f 3 > result
diff -q -b result expected
rm -f expected result input
# gotree annotate
echo "->gotree annotate"
cat > mapfile <<EOF
internal1:Tip6,Tip5,Tip1
EOF
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)internal1));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} brlen clear | ${GOTREE} annotate -m mapfile > result
diff -q -b result expected
rm -f expected result mapfile
# gotree annotate
echo "->gotree annotate 2"
cat > mapfile <<EOF
ACGACTCATCTA:Tip6,Tip5,Tip1
ACGACTCATCTA:internal1
EOF
cat > intree <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3))internal1,((Tip6,Tip5),Tip1)));
EOF
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3))ACGACTCATCTA,((Tip6,Tip5),Tip1)ACGACTCATCTA));
EOF
${GOTREE} annotate -i intree -m mapfile > result
diff -q -b result expected
rm -f expected result intree mapfile
# gotree annotate
echo "->gotree annotate comment"
cat > mapfile <<EOF
internal1:Tip6,Tip5,Tip1
EOF
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)[internal1]));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} brlen clear | ${GOTREE} annotate --comment -m mapfile > result
diff -q -b result expected
rm -f expected result mapfile
# gotree annotate
echo "->gotree annotate comment 2"
cat > mapfile <<EOF
ACGACTCATCTA:Tip6,Tip5,Tip1
ACGACTCATCTA:internal1
EOF
cat > intree <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3))internal1,((Tip6,Tip5),Tip1)));
EOF
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3))internal1[ACGACTCATCTA],((Tip6,Tip5),Tip1)[ACGACTCATCTA]));
EOF
${GOTREE} annotate -i intree --comment -m mapfile > result
diff -q -b result expected
rm -f expected result intree mapfile
# gotree annotate with tree
echo "->gotree annotate with tree"
cat > intree <<EOF
((Tip4,(Tip7,Tip2)n1)n2,Tip0,((Tip8,(Tip9,Tip3)n3)n4,((Tip6,Tip1)n5,Tip5)n6)n7);
EOF
cat > expected1 <<EOF
((Tip4,(Tip7,Tip2)n1_0_2)n2_0_3,Tip0,((Tip8,(Tip9,Tip3)n3_0_2)n4_0_3,((Tip6,Tip5),Tip1)n6_0_3)n7_0_6);
EOF
cat > expected2 <<EOF
((Tip4,(Tip7,Tip2)n1_0_2)n2_0_3,Tip0,((Tip8,(Tip9,Tip3)n3_0_2)n4_0_3,((Tip6,Tip5)n6_1_2,Tip1)n6_0_3)n7_0_6);
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} brlen clear | ${GOTREE} annotate -c intree > result
diff -q -b result expected1 || diff -q -b result expected2
rm -f expected1 expected2 result intree
# gotree annotate with tree
echo "->gotree annotate with tree comments"
cat > intree <<EOF
((Tip4,(Tip7,Tip2)n1)n2,Tip0,((Tip8,(Tip9,Tip3)n3)n4,((Tip6,Tip1)n5,Tip5)n6)n7);
EOF
cat > expected1 <<EOF
((Tip4,(Tip7,Tip2)[n1_0_2])[n2_0_3],Tip0,((Tip8,(Tip9,Tip3)[n3_0_2])[n4_0_3],((Tip6,Tip5),Tip1)[n6_0_3])[n7_0_6]);
EOF
cat > expected2 <<EOF
((Tip4,(Tip7,Tip2)[n1_0_2])[n2_0_3],Tip0,((Tip8,(Tip9,Tip3)[n3_0_2])[n4_0_3],((Tip6,Tip5)[n6_1_2],Tip1)[n6_0_3])[n7_0_6]);
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} brlen clear | ${GOTREE} annotate --comment -c intree > result
diff -q -b result expected1 || diff -q -b result expected2
rm -f expected result intree
# gotree brlen clear
echo "->gotree brlen clear"
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)));
(Tip5,Tip0,((Tip6,(Tip7,Tip4)),(Tip2,((Tip8,(Tip9,Tip3)),Tip1))));
(Tip6,Tip0,((((Tip5,Tip4),((Tip9,Tip8),Tip3)),(Tip7,Tip2)),Tip1));
(Tip3,Tip0,(((Tip6,Tip5),Tip2),(((Tip9,Tip8),Tip4),(Tip7,Tip1))));
(((Tip4,(Tip8,Tip3)),((Tip6,Tip5),Tip2)),Tip0,(Tip7,(Tip9,Tip1)));
(Tip4,Tip0,(Tip3,((((Tip8,Tip7),Tip5),((Tip9,Tip6),Tip2)),Tip1)));
(Tip5,Tip0,((Tip8,Tip2),((Tip7,Tip3),((Tip9,Tip4),(Tip6,Tip1)))));
((Tip9,Tip6),Tip0,((((Tip8,Tip4),Tip3),Tip2),((Tip7,Tip5),Tip1)));
(Tip9,Tip0,(Tip8,((Tip7,Tip4),((Tip6,Tip2),(Tip3,(Tip5,Tip1))))));
((((Tip7,(Tip8,(Tip9,Tip6))),Tip5),Tip4),Tip0,(Tip2,(Tip3,Tip1)));
EOF
${GOTREE} generate yuletree --seed 10 -n 10 | ${GOTREE} brlen clear > result
diff -q -b result expected
rm -f expected result
# gotree brlen scale
echo "->gotree brlen scale"
cat > input.tree <<EOF
((Tip4:1,(Tip7:1,Tip2:1):1):1,Tip0:1,((Tip8:1,(Tip9:1,Tip3:1):1):1,((Tip6:1,Tip5:1):1,Tip1:1):1):1);
(Tip5,Tip0,((Tip6,(Tip7,Tip4)),(Tip2,((Tip8,(Tip9,Tip3)),Tip1))));
(Tip6:0.5,Tip0:0.5,((((Tip5:0.5,Tip4:0.5):0.5,((Tip9:0.5,Tip8:0.5),Tip3:0.5):0.5):0.5,(Tip7:0.5,Tip2:0.5):0.5):0.5,Tip1:0.5):0.5);
EOF
cat > expected <<EOF
((Tip4:3,(Tip7:3,Tip2:3):3):3,Tip0:3,((Tip8:3,(Tip9:3,Tip3:3):3):3,((Tip6:3,Tip5:3):3,Tip1:3):3):3);
(Tip5,Tip0,((Tip6,(Tip7,Tip4)),(Tip2,((Tip8,(Tip9,Tip3)),Tip1))));
(Tip6:1.5,Tip0:1.5,((((Tip5:1.5,Tip4:1.5):1.5,((Tip9:1.5,Tip8:1.5),Tip3:1.5):1.5):1.5,(Tip7:1.5,Tip2:1.5):1.5):1.5,Tip1:1.5):1.5);
EOF
${GOTREE} brlen scale -i input.tree -f 3.0 > result
diff -q -b result expected
rm -f expected result input.tree
# gotree support scale
echo "->gotree support scale"
cat > input.tree <<EOF
((a,b)99,(c,d)50,(e,f)0,g);
EOF
cat > expected.1 <<EOF
((a,b)0.99,(c,d)0.5,(e,f)0,g);
EOF
cat > expected.2 <<EOF
((a,b)198,(c,d)100,(e,f)0,g);
EOF
${GOTREE} support scale -i input.tree -f 0.01 > result.1
${GOTREE} support scale -i input.tree -f 2 > result.2
diff -q -b result.1 expected.1
diff -q -b result.2 expected.2
rm -f expected.1 expected.2 result.1 result.2 input.tree
# gotree support clear
echo "->gotree support clear"
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)));
(Tip5,Tip0,((Tip6,(Tip7,Tip4)),(Tip2,((Tip8,(Tip9,Tip3)),Tip1))));
(Tip6,Tip0,((((Tip5,Tip4),((Tip9,Tip8),Tip3)),(Tip7,Tip2)),Tip1));
(Tip3,Tip0,(((Tip6,Tip5),Tip2),(((Tip9,Tip8),Tip4),(Tip7,Tip1))));
(((Tip4,(Tip8,Tip3)),((Tip6,Tip5),Tip2)),Tip0,(Tip7,(Tip9,Tip1)));
(Tip4,Tip0,(Tip3,((((Tip8,Tip7),Tip5),((Tip9,Tip6),Tip2)),Tip1)));
(Tip5,Tip0,((Tip8,Tip2),((Tip7,Tip3),((Tip9,Tip4),(Tip6,Tip1)))));
((Tip9,Tip6),Tip0,((((Tip8,Tip4),Tip3),Tip2),((Tip7,Tip5),Tip1)));
(Tip9,Tip0,(Tip8,((Tip7,Tip4),((Tip6,Tip2),(Tip3,(Tip5,Tip1))))));
((((Tip7,(Tip8,(Tip9,Tip6))),Tip5),Tip4),Tip0,(Tip2,(Tip3,Tip1)));
EOF
${GOTREE} generate yuletree --seed 10 -n 10 | ${GOTREE} support setrand | ${GOTREE} support clear | ${GOTREE} brlen clear > result
diff -q -b result expected
rm -f expected result
# gotree comment clear
echo "->gotree comment clear"
cat > input <<EOF
(t1[c1],t2[c2],(t3[c3],t4[c4])[c5]);
EOF
cat > expected <<EOF
(t1,t2,(t3,t4));
EOF
${GOTREE} comment clear -i input > result
diff -q -b result expected
rm -f expected result input
# gotree comment clear nodes+edges
echo "->gotree comment clear (nodes+edges)"
cat > input <<EOF
(t1[n1]:1[e1],t2[n2]:1[e2],(t3[n3]:1[e3],t4[n4]:1[e4])[n5]:1[e5]);
EOF
cat > expected <<EOF
(t1:1,t2:1,(t3:1,t4:1):1);
EOF
${GOTREE} comment clear -i input > result
diff -q -b result expected
rm -f expected result input
# gotree comment clear nodes only
echo "->gotree comment clear (nodes)"
cat > input <<EOF
(t1[n1]:1[e1],t2[n2]:1[e2],(t3[n3]:1[e3],t4[n4]:1[e4])[n5]:1[e5]);
EOF
cat > expected <<EOF
(t1:1[e1],t2:1[e2],(t3:1[e3],t4:1[e4]):1[e5]);
EOF
${GOTREE} comment clear --nodes-only -i input > result
diff -q -b result expected
rm -f expected result input
# gotree comment clear edges only
echo "->gotree comment clear (edges)"
cat > input <<EOF
(t1[n1]:1[e1],t2[n2]:1[e2],(t3[n3]:1[e3],t4[n4]:1[e4])[n5]:1[e5]);
EOF
cat > expected <<EOF
(t1[n1]:1,t2[n2]:1,(t3[n3]:1,t4[n4]:1)[n5]:1);
EOF
${GOTREE} comment clear --edges-only -i input > result
diff -q -b result expected
rm -f expected result input
# gotree comment transfer
echo "->gotree comment transfer"
cat > input <<EOF
(t1:1,t2:1,(t3:1,t4:1)n5:1);
EOF
cat > expected <<EOF
(t1:1,t2:1,(t3:1,t4:1)[n5]:1);
EOF
${GOTREE} comment transfer -i input > result
diff -q -b result expected
rm -f expected result input
# gotree comment transfer --reverse
echo "->gotree comment transfer --reverse"
cat > input <<EOF
(t1:1,t2:1,(t3:1,t4:1)[n5]:1);
EOF
cat > expected <<EOF
(t1:1,t2:1,(t3:1,t4:1)n5:1);
EOF
${GOTREE} comment transfer --reverse -i input > result
diff -q -b result expected
rm -f expected result input
# gotree collapse length
echo "->gotree collapse length"
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),Tip0,(Tip8,Tip9,Tip3),((Tip6,Tip5),Tip1));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} collapse length -l 0.05 | ${GOTREE} brlen clear > result
diff -q -b result expected
rm -f expected result
echo "->gotree collapse support root + tips"
cat > expected <<EOF
(A:1,B:1,C:1,D:1);
EOF
echo "((A:1,B:1)0.2:1,(C:1,D:1)0.1:1);" | ${GOTREE} collapse support -s 1 --root > result
diff -q -b result expected
rm -f expected result
echo "->gotree collapse length root + tips"
cat > expected <<EOF
(A:0,B:0,C:0,D:0);
EOF
echo "((A:1,B:1)0.2:1,(C:1,D:1)0.1:1);" | ${GOTREE} collapse length -l 2 --root --tips > result
diff -q -b result expected
rm -f expected result
echo "->gotree collapse depth root + tips"
cat > expected <<EOF
(A:0,B:0,C:0,D:0);
EOF
echo "((A:1,B:1)0.2:1,(C:1,D:1)0.1:1);" | ${GOTREE} collapse depth -m 0 -M 10 --root --tips > result
diff -q -b result expected
rm -f expected result
# gotree collapse support
echo "->gotree collapse support"
cat > expected <<EOF
(Tip0,((Tip1,Tip6,Tip5)0.9167074899036827,Tip8,Tip9,Tip3)0.925128845219594,Tip4,Tip7,Tip2);
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} support setrand --seed 10 | ${GOTREE} collapse support -s 0.7 | ${GOTREE} brlen clear > result
diff -q -b result expected
rm -f expected result
# gotree collapse depth
echo "->gotree collapse depth"
cat > expected <<EOF
((Tip4,Tip7,Tip2),Tip0,((Tip8,Tip9,Tip3),(Tip1,Tip6,Tip5)));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} collapse depth -m 2 -M 2 | ${GOTREE} brlen clear > result
diff -q -b result expected
rm -f expected result
# gotree collapse id
echo "->gotree collapse id/name"
cat > input <<EOF
((Tip4,Tip7,Tip2),Tip0,((Tip8,Tip9,Tip3),(Tip1,Tip6,Tip5)));
EOF
cat > expected <<EOF
(Tip0,Tip4,Tip7,Tip2,Tip8,Tip9,Tip3,Tip1,Tip6,Tip5);
EOF
cat > expected2 <<EOF
(Tip0,Tip4,Tip7,Tip2,(Tip1,Tip6,Tip5),Tip8,Tip9,Tip3);
EOF
cat > br <<EOF
0
5
6
10
EOF
cat > br2 <<EOF
0
5
6
EOF
${GOTREE} collapse name -i input --id -b br > result
diff -q -b result expected
${GOTREE} collapse name -i input --id -b br2 > result
diff -q -b result expected2
rm -f input expected result br br2 expected2
# gotree collapse single
echo "->gotree collapse single"
cat > test_input <<EOF
((((A,B)),((C))),(D,(E)));
EOF
cat > expected <<EOF
(((A,B),C),(D,E));
EOF
${GOTREE} collapse single -i test_input > result
diff -q -b result expected
rm -f expected result test_input
# gotree compare trees
echo "->gotree compare trees"
cat > expected <<EOF
tree reference common compared
0 7 0 7
EOF
${GOTREE} compare trees -i <(${GOTREE} generate yuletree --seed 10) -c <(${GOTREE} generate yuletree --seed 12 -n 1) > result
diff -q -b expected result
rm -f expected result
# gotree compare trees weighted
echo "->gotree compare trees weighted"
cat > input <<EOF
(A:0.1,(B:0.1,(H:0.1,(D:0.1,(J:0.1,(((G:0.1,E:0.1):0.1,(F:0.1,I:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(D:0.1,((J:0.1,H:0.1):0.1,(((G:0.1,E:0.1):0.1,(F:0.1,I:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(D:0.1,(H:0.1,(J:0.1,(((G:0.1,E:0.1):0.1,(F:0.1,I:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,(G:0.1,((F:0.1,I:0.1):0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,(G:0.1,((F:0.1,I:0.1):0.1,(((J:0.1,H:0.1):0.1,D:0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,((F:0.1,I:0.1):0.1,(G:0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,((F:0.1,I:0.1):0.1,(G:0.1,(((J:0.1,H:0.1):0.1,D:0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,((G:0.1,(F:0.1,I:0.1):0.1):0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,((G:0.1,(F:0.1,I:0.1):0.1):0.1,(((J:0.1,H:0.1):0.1,D:0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,(G:0.1,((F:0.1,I:0.1):0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(D:0.1,(H:0.1,(J:0.1,(((G:0.1,E:0.1):0.1,(F:0.1,I:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1):0.1);
(A:0.1,(B:0.1,(E:0.1,((G:0.1,(F:0.1,I:0.1):0.1):0.1,((J:0.1,(H:0.1,D:0.1):0.1):0.1,C:0.1):0.1):0.1):0.1):0.1);
EOF
cat > expected <<EOF
KF KF KF KF KF KF KF KF KF KF KF KF
0.000000E+00 2.000000E-01 1.414214E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 1.414214E-01 3.162278E-01
2.000000E-01 0.000000E+00 1.414214E-01 3.162278E-01 2.828427E-01 3.162278E-01 2.828427E-01 3.162278E-01 2.828427E-01 3.162278E-01 1.414214E-01 3.162278E-01
1.414214E-01 1.414214E-01 0.000000E+00 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 0.000000E+00 3.162278E-01
3.162278E-01 3.162278E-01 3.162278E-01 0.000000E+00 1.414214E-01 1.414214E-01 2.000000E-01 1.414214E-01 2.000000E-01 0.000000E+00 3.162278E-01 1.414214E-01
3.162278E-01 2.828427E-01 3.162278E-01 1.414214E-01 0.000000E+00 2.000000E-01 1.414214E-01 2.000000E-01 1.414214E-01 1.414214E-01 3.162278E-01 2.000000E-01
3.162278E-01 3.162278E-01 3.162278E-01 1.414214E-01 2.000000E-01 0.000000E+00 1.414214E-01 1.414214E-01 2.000000E-01 1.414214E-01 3.162278E-01 1.414214E-01
3.162278E-01 2.828427E-01 3.162278E-01 2.000000E-01 1.414214E-01 1.414214E-01 0.000000E+00 2.000000E-01 1.414214E-01 2.000000E-01 3.162278E-01 2.000000E-01
3.162278E-01 3.162278E-01 3.162278E-01 1.414214E-01 2.000000E-01 1.414214E-01 2.000000E-01 0.000000E+00 1.414214E-01 1.414214E-01 3.162278E-01 0.000000E+00
3.162278E-01 2.828427E-01 3.162278E-01 2.000000E-01 1.414214E-01 2.000000E-01 1.414214E-01 1.414214E-01 0.000000E+00 2.000000E-01 3.162278E-01 1.414214E-01
3.162278E-01 3.162278E-01 3.162278E-01 0.000000E+00 1.414214E-01 1.414214E-01 2.000000E-01 1.414214E-01 2.000000E-01 0.000000E+00 3.162278E-01 1.414214E-01
1.414214E-01 1.414214E-01 0.000000E+00 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 3.162278E-01 0.000000E+00 3.162278E-01
3.162278E-01 3.162278E-01 3.162278E-01 1.414214E-01 2.000000E-01 1.414214E-01 2.000000E-01 0.000000E+00 1.414214E-01 1.414214E-01 3.162278E-01 0.000000E+00
EOF
var=1
while IFS= read -r line; do
echo "$line" | ${GOTREE} compare trees --weighted -c input | cut -d $'\t' -f3 > $var.txt
var=$((var + 1))
done < input
# Make a pretty table
paste {1,2,3,4,5,6,7,8,9,10,11,12}.txt > result
# Remove temp files
rm {1,2,3,4,5,6,7,8,9,10,11,12}.txt
diff -q -b expected result
rm -f expected input result
# gotree compare edges
echo "->gotree compare edges"
cat > expected <<EOF
tree brid length support terminal depth topodepth rootdepth rightname found comment transfer taxatomove comparednodename comparedlength comparedsupport comparedtopodepth comparedid comparedcomment
0 0 0.1824683850061218 N/A false 1 3 -1 false [] 2 +Tip4,+Tip2 Tip7 0.2281203179753742 N/A 1 14 []
0 1 0.020616211789029896 N/A true 0 1 -1 Tip4 true [] 0 Tip4 0.32980883896257585 N/A 1 2 []
0 2 0.25879284932877245 N/A false 1 2 -1 false [] 1 +Tip2 Tip7 0.2281203179753742 N/A 1 14 []
0 3 0.09740195047110385 N/A true 0 1 -1 Tip7 true [] 0 Tip7 0.2281203179753742 N/A 1 14 []
0 4 0.015450672710905129 N/A true 0 1 -1 Tip2 true [] 0 Tip2 0.037584651176611125 N/A 1 11 []
0 5 0.25919865790518115 N/A true 0 1 -1 Tip0 true [] 0 Tip0 0.11291296397843323 N/A 1 3 []
0 6 0.04593880904706901 N/A false 1 4 -1 false [] 3 +Tip2,+Tip7,-Tip6 0.05806229063227526 N/A 3 4 []
0 7 0.1920960924280275 N/A false 1 3 -1 false [] 1 +Tip3 0.005131510752894519 N/A 2 8 []
0 8 0.027845992087631298 N/A true 0 1 -1 Tip8 true [] 0 Tip8 0.060367242116658816 N/A 1 10 []
0 9 0.01026581233891113 N/A false 1 2 -1 false [] 1 +Tip3 Tip9 0.16045157517594316 N/A 1 9 []
0 10 0.13492605122032592 N/A true 0 1 -1 Tip9 true [] 0 Tip9 0.16045157517594316 N/A 1 9 []
0 11 0.10309294031874587 N/A true 0 1 -1 Tip3 true [] 0 Tip3 0.35163191615522493 N/A 1 5 []
0 12 0.30150414585026103 N/A false 1 3 -1 false [] 2 +Tip6,-Tip7 0.12937482578337411 N/A 3 12 []
0 13 0.05817538156872999 N/A false 1 2 -1 false [] 1 +Tip6 Tip5 0.054439044275040135 N/A 1 15 []
0 14 0.3779897840448691 N/A true 0 1 -1 Tip6 true [] 0 Tip6 0.05325654013915672 N/A 1 1 []
0 15 0.1120177846434196 N/A true 0 1 -1 Tip5 true [] 0 Tip5 0.054439044275040135 N/A 1 15 []
0 16 0.239082088939295 N/A true 0 1 -1 Tip1 true [] 0 Tip1 0.013105562909283169 N/A 1 16 []
EOF
${GOTREE} compare edges -i <(${GOTREE} generate yuletree --seed 10) -c <(${GOTREE} generate yuletree --seed 12 -n 1) -m --moved-taxa > result 2>/dev/null
diff -q -b expected result
rm -f expected result
# gotree compare edges
echo "->gotree compare edges /2 (same tree)"
cat > expected <<EOF
tree brid length support terminal depth topodepth rootdepth rightname found comment transfer taxatomove comparednodename comparedlength comparedsupport comparedtopodepth comparedid comparedcomment
0 0 0.1824683850061218 N/A false 1 3 -1 true [] 0 0.1824683850061218 N/A 3 0 []
0 1 0.020616211789029896 N/A true 0 1 -1 Tip4 true [] 0 Tip4 0.020616211789029896 N/A 1 1 []
0 2 0.25879284932877245 N/A false 1 2 -1 true [] 0 0.25879284932877245 N/A 2 2 []
0 3 0.09740195047110385 N/A true 0 1 -1 Tip7 true [] 0 Tip7 0.09740195047110385 N/A 1 3 []
0 4 0.015450672710905129 N/A true 0 1 -1 Tip2 true [] 0 Tip2 0.015450672710905129 N/A 1 4 []
0 5 0.25919865790518115 N/A true 0 1 -1 Tip0 true [] 0 Tip0 0.25919865790518115 N/A 1 5 []
0 6 0.04593880904706901 N/A false 1 4 -1 true [] 0 0.04593880904706901 N/A 4 6 []
0 7 0.1920960924280275 N/A false 1 3 -1 true [] 0 0.1920960924280275 N/A 3 7 []
0 8 0.027845992087631298 N/A true 0 1 -1 Tip8 true [] 0 Tip8 0.027845992087631298 N/A 1 8 []
0 9 0.01026581233891113 N/A false 1 2 -1 true [] 0 0.01026581233891113 N/A 2 9 []
0 10 0.13492605122032592 N/A true 0 1 -1 Tip9 true [] 0 Tip9 0.13492605122032592 N/A 1 10 []
0 11 0.10309294031874587 N/A true 0 1 -1 Tip3 true [] 0 Tip3 0.10309294031874587 N/A 1 11 []
0 12 0.30150414585026103 N/A false 1 3 -1 true [] 0 0.30150414585026103 N/A 3 12 []
0 13 0.05817538156872999 N/A false 1 2 -1 true [] 0 0.05817538156872999 N/A 2 13 []
0 14 0.3779897840448691 N/A true 0 1 -1 Tip6 true [] 0 Tip6 0.3779897840448691 N/A 1 14 []
0 15 0.1120177846434196 N/A true 0 1 -1 Tip5 true [] 0 Tip5 0.1120177846434196 N/A 1 15 []
0 16 0.239082088939295 N/A true 0 1 -1 Tip1 true [] 0 Tip1 0.239082088939295 N/A 1 16 []
EOF
${GOTREE} compare edges -i <(${GOTREE} generate yuletree --seed 10) -c <(${GOTREE} generate yuletree --seed 10 -n 1) -m --moved-taxa > result 2>/dev/null
diff -q -b expected result
rm -f expected result
# gotree compare tips
echo "->gotree compare tips"
cat > expected <<EOF
(Tree 0) > Tip11
(Tree 0) > Tip10
(Tree 0) = 10
EOF
${GOTREE} compare tips -i <(${GOTREE} generate yuletree --seed 10) -c <(${GOTREE} generate yuletree --seed 12 -n 1 -l 12) > result
diff -q -b expected result
rm -f expected result
# gotree compare tips file
echo "->gotree compare tips file"
cat > expected <<EOF
(Tree 0) > Tip11
(Tree 0) > Tip10
(Tree 0) = 10
EOF
cat > tipfile <<EOF
Tip0
Tip1
Tip2
Tip3
Tip4
Tip5
Tip6
Tip7
Tip8
Tip9
Tip11
Tip10
EOF
${GOTREE} compare tips -i <(${GOTREE} generate yuletree --seed 10) -f tipfile > result
diff -q -b <(sort expected) <(sort result)
rm -f expected result
# # gotree compare distances
# echo "->gotree compare distances"
# cat > expected <<EOF
# tree_id er_id ec_id tdist ec_length ec_support ec_topodepth moving_taxa
# 0 0 0 3 0.018862750655150758 N/A 2 +Tip6,-Tip2,-Tip7
# 0 0 4 4 0.05806229063227526 N/A 3 +Tip0,+Tip6,-Tip2,-Tip7
# 0 0 6 5 0.006167968511774678 N/A 4 +Tip0,+Tip3,+Tip6,-Tip2,-Tip7
# 0 0 7 4 0.03856952076464118 N/A 3 +Tip8,+Tip9,-Tip4,-Tip7
# 0 0 8 5 0.005131510752894519 N/A 2 +Tip0,+Tip1,+Tip3,+Tip5,+Tip6
# 0 0 12 4 0.12937482578337411 N/A 3 +Tip1,+Tip5,-Tip2,-Tip4
# 0 0 13 3 0.00518311446616857 N/A 2 +Tip5,-Tip2,-Tip4
# 0 2 0 4 0.018862750655150758 N/A 2 +Tip4,+Tip6,-Tip2,-Tip7
# 0 2 4 5 0.05806229063227526 N/A 3 +Tip0,+Tip4,+Tip6,-Tip2,-Tip7
# 0 2 6 4 0.006167968511774678 N/A 4 +Tip1,+Tip5,+Tip8,+Tip9
# 0 2 7 3 0.03856952076464118 N/A 3 +Tip8,+Tip9,-Tip7
# 0 2 8 4 0.005131510752894519 N/A 2 +Tip8,+Tip9,-Tip2,-Tip7
# 0 2 12 3 0.12937482578337411 N/A 3 +Tip1,+Tip5,-Tip2
# 0 2 13 2 0.00518311446616857 N/A 2 +Tip5,-Tip2
# 0 6 0 4 0.018862750655150758 N/A 2 +Tip0,+Tip2,+Tip7,-Tip6
# 0 6 4 3 0.05806229063227526 N/A 3 +Tip2,+Tip7,-Tip6
# 0 6 6 4 0.006167968511774678 N/A 4 +Tip2,+Tip7,-Tip3,-Tip6
# 0 6 7 5 0.03856952076464118 N/A 3 +Tip0,+Tip4,+Tip7,-Tip8,-Tip9
# 0 6 8 4 0.005131510752894519 N/A 2 -Tip1,-Tip3,-Tip5,-Tip6
# 0 6 12 5 0.12937482578337411 N/A 3 +Tip0,+Tip2,+Tip4,-Tip1,-Tip5
# 0 6 13 4 0.00518311446616857 N/A 2 +Tip0,+Tip2,+Tip4,-Tip5
# 0 7 0 5 0.018862750655150758 N/A 2 +Tip0,+Tip1,+Tip2,+Tip5,+Tip7
# 0 7 4 4 0.05806229063227526 N/A 3 +Tip1,+Tip2,+Tip5,+Tip7
# 0 7 6 5 0.006167968511774678 N/A 4 +Tip0,+Tip4,+Tip6,-Tip8,-Tip9
# 0 7 7 2 0.03856952076464118 N/A 3 +Tip2,-Tip3
# 0 7 8 1 0.005131510752894519 N/A 2 -Tip3
# 0 7 12 4 0.12937482578337411 N/A 3 +Tip0,+Tip2,+Tip4,+Tip6
# 0 7 13 5 0.00518311446616857 N/A 2 +Tip0,+Tip1,+Tip2,+Tip4,+Tip6
# 0 9 0 4 0.018862750655150758 N/A 2 +Tip4,+Tip6,-Tip3,-Tip9
# 0 9 4 5 0.05806229063227526 N/A 3 +Tip0,+Tip4,+Tip6,-Tip3,-Tip9
# 0 9 6 4 0.006167968511774678 N/A 4 +Tip0,+Tip4,+Tip6,-Tip9
# 0 9 7 3 0.03856952076464118 N/A 3 +Tip2,+Tip8,-Tip3
# 0 9 8 2 0.005131510752894519 N/A 2 +Tip8,-Tip3
# 0 9 12 5 0.12937482578337411 N/A 3 +Tip0,+Tip2,+Tip4,+Tip6,+Tip8
# 0 9 13 4 0.00518311446616857 N/A 2 +Tip5,+Tip7,-Tip3,-Tip9
# 0 12 0 3 0.018862750655150758 N/A 2 +Tip4,-Tip1,-Tip5
# 0 12 4 4 0.05806229063227526 N/A 3 +Tip0,+Tip4,-Tip1,-Tip5
# 0 12 6 5 0.006167968511774678 N/A 4 +Tip0,+Tip3,+Tip4,-Tip1,-Tip5
# 0 12 7 4 0.03856952076464118 N/A 3 +Tip0,+Tip3,+Tip4,+Tip7
# 0 12 8 5 0.005131510752894519 N/A 2 +Tip0,+Tip2,+Tip3,+Tip4,+Tip7
# 0 12 12 2 0.12937482578337411 N/A 3 +Tip7,-Tip6
# 0 12 13 3 0.00518311446616857 N/A 2 +Tip7,-Tip1,-Tip6
# 0 13 0 2 0.018862750655150758 N/A 2 +Tip4,-Tip5
# 0 13 4 3 0.05806229063227526 N/A 3 +Tip0,+Tip4,-Tip5
# 0 13 6 4 0.006167968511774678 N/A 4 +Tip0,+Tip3,+Tip4,-Tip5
# 0 13 7 5 0.03856952076464118 N/A 3 +Tip0,+Tip1,+Tip3,+Tip4,+Tip7
# 0 13 8 4 0.005131510752894519 N/A 2 +Tip8,+Tip9,-Tip5,-Tip6
# 0 13 12 3 0.12937482578337411 N/A 3 +Tip1,+Tip7,-Tip6
# 0 13 13 2 0.00518311446616857 N/A 2 +Tip7,-Tip6
# EOF
# ${GOTREE} compare distances -i <(${GOTREE} generate yuletree --seed 10) -c <(${GOTREE} generate yuletree --seed 12 -n 1) > result 2>/dev/null
# diff -q -b expected result
# rm -f expected result
# goree compute bipartitiontree
echo "->gotree compute bipartitiontree"
cat > expected <<EOF
((Tip4:1,Tip7:1,Tip0:1,Tip8:1,Tip9:1,Tip6:1,Tip5:1):1,Tip1:1,Tip2:1,Tip3:1);
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} compute bipartitiontree Tip1 Tip2 Tip3 > result
diff -q -b expected result
rm -f result expected
# gotree compute consensus
echo "->gotree compute consensus"
cat > expected_comp <<EOF
tree reference common compared
0 0 5 0
EOF
cat > expected_tree <<EOF
(Tip0:0.12347870000000004,(Tip9:0.12811019999999992,(Tip8:0.018413999999999993,Tip3:0.10146340000000001)0.87:0.012998850574712643)1:0.08962310000000002,(Tip1:0.17112029999999998,Tip6:0.30890189999999984,Tip5:0.0929547)0.97:0.07447020618556698,(Tip4:0.030012499999999987,(Tip7:0.09010099999999997,Tip2:0.015264200000000006)1:0.10734890000000002)1:0.09298299999999998);
EOF
${GOTREE} compute consensus -i ${TESTDATA}/bootstap_test.nw.gz -f 0.7 | ${GOTREE} compare trees -i expected_tree -c - > result
diff -q -b expected_comp result
rm -f expected_comp expected_tree result
echo "->gotree compute classical bootstrap"
cat > expected <<EOF
(Tip0,(Tip4,(Tip7,Tip2)1)1,((Tip9,(Tip8,Tip3)0.87)1,(Tip1,(Tip6,Tip5)0.65)0.97)0.67);
EOF
${GOTREE} compute support fbp -i ${TESTDATA}/bootstap_inferred_test.nw.gz -b ${TESTDATA}/bootstap_test.nw.gz 2>/dev/null | ${GOTREE} brlen clear > result
diff -q -b expected result
${GOTREE} compute support classical -i ${TESTDATA}/bootstap_inferred_test.nw.gz -b ${TESTDATA}/bootstap_test.nw.gz 2>/dev/null | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result
echo "->gotree compute booster supports"
cat > expected <<EOF
(Tip0,(Tip4,(Tip7,Tip2)1)1,((Tip9,(Tip8,Tip3)0.87)1,(Tip1,(Tip6,Tip5)0.65)0.985)0.89);
EOF
${GOTREE} compute support booster -i ${TESTDATA}/bootstap_inferred_test.nw.gz -b ${TESTDATA}/bootstap_test.nw.gz --silent -l /dev/null | ${GOTREE} brlen clear > result
diff -q -b expected result
${GOTREE} compute support tbe -i ${TESTDATA}/bootstap_inferred_test.nw.gz -b ${TESTDATA}/bootstap_test.nw.gz --silent -l /dev/null | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result
echo "->gotree compute edgetrees"
cat > expected <<EOF
((Tip4:1,Tip7:1,Tip2:1):1,Tip0:1,Tip8:1,Tip9:1,Tip3:1,Tip6:1,Tip5:1,Tip1:1);
((Tip7:1,Tip2:1):1,Tip4:1,Tip0:1,Tip8:1,Tip9:1,Tip3:1,Tip6:1,Tip5:1,Tip1:1);
((Tip8:1,Tip9:1,Tip3:1,Tip6:1,Tip5:1,Tip1:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1);
((Tip8:1,Tip9:1,Tip3:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip6:1,Tip5:1,Tip1:1);
((Tip9:1,Tip3:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip8:1,Tip6:1,Tip5:1,Tip1:1);
((Tip6:1,Tip5:1,Tip1:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip8:1,Tip9:1,Tip3:1);
((Tip6:1,Tip5:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip8:1,Tip9:1,Tip3:1,Tip1:1);
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} compute edgetrees > result
diff -q -b expected result
rm -f expected result
echo "->gotree compute edgetrees"
cat > expected <<EOF
((Tip4:1,Tip7:1,Tip2:1):1,Tip0:1,Tip8:1,Tip9:1,Tip3:1,Tip6:1,Tip5:1,Tip1:1);
((Tip7:1,Tip2:1):1,Tip4:1,Tip0:1,Tip8:1,Tip9:1,Tip3:1,Tip6:1,Tip5:1,Tip1:1);
((Tip8:1,Tip9:1,Tip3:1,Tip6:1,Tip5:1,Tip1:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1);
((Tip8:1,Tip9:1,Tip3:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip6:1,Tip5:1,Tip1:1);
((Tip9:1,Tip3:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip8:1,Tip6:1,Tip5:1,Tip1:1);
((Tip6:1,Tip5:1,Tip1:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip8:1,Tip9:1,Tip3:1);
((Tip6:1,Tip5:1):1,Tip4:1,Tip7:1,Tip2:1,Tip0:1,Tip8:1,Tip9:1,Tip3:1,Tip1:1);
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} compute edgetrees > result
diff -q -b expected result
rm -f expected result
echo "->gotree divide"
cat > expected1 <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)));
EOF
cat > expected2 <<EOF
(Tip5,Tip0,((Tip6,(Tip7,Tip4)),(Tip2,((Tip8,(Tip9,Tip3)),Tip1))));
EOF
${GOTREE} generate yuletree --seed 10 -n 2 | ${GOTREE} brlen clear | ${GOTREE} divide -o div
diff -q -b expected1 div_000.nw
diff -q -b expected2 div_001.nw
rm -f expected1 expected2 div_000.nw div_001.nw
echo "->gotree generate yuletree"
cat > expected <<EOF
((Tip4:0.020616211789029896,(Tip7:0.09740195047110385,Tip2:0.015450672710905129):0.25879284932877245):0.1824683850061218,Tip0:0.25919865790518115,((Tip8:0.027845992087631298,(Tip9:0.13492605122032592,Tip3:0.10309294031874587):0.01026581233891113):0.1920960924280275,((Tip6:0.3779897840448691,Tip5:0.1120177846434196):0.05817538156872999,Tip1:0.239082088939295):0.30150414585026103):0.04593880904706901);
EOF
${GOTREE} generate yuletree --seed 10 -n 1 > result
diff -q -b expected result
rm -f expected result
echo "->gotree generate balancedtree"
cat > expected <<EOF
(((Tip0:0.04593880904706901,Tip1:0.13604994737755394):0.06718605070537677,(Tip2:0.19852695409349608,Tip3:0.002749016032849596):0.2485396648662035):0.25919865790518115,((Tip4:0.12467449897149811,Tip5:0.10033210749794116):0.1824683850061218,(Tip6:0.30150414585026103,Tip7:0.08184535681853511):0.020616211789029896):0.054743875470795914,(((Tip8:0.1120177846434196,Tip9:0.18347097513974125):0.05817538156872999,(Tip10:0.25879284932877245,Tip11:0.09740195047110385):0.3779897840448691):0.239082088939295,((Tip12:0.1920960924280275,Tip13:0.027845992087631298):0.015450672710905129,(Tip14:0.0440885662122905,Tip15:0.14809735366802398):0.17182241382980687):0.03199874235185574):0.13756099791982077);
EOF
${GOTREE} generate balancedtree --seed 10 -d 4 > result
diff -q -b expected result
rm -f expected result
echo "->gotree generate caterpillartree"
cat > expected <<EOF
((((((((Tip9:0.09740195047110385,Tip8:0.015450672710905129):0.25879284932877245,Tip7:0.18347097513974125):0.3779897840448691,Tip6:0.05817538156872999):0.239082088939295,Tip5:0.08184535681853511):0.10033210749794116,Tip4:0.12467449897149811):0.1824683850061218,Tip3:0.002749016032849596):0.13604994737755394,Tip2:0.04593880904706901):0.06718605070537677,Tip0:0.0540687078328298,Tip1:0.054743875470795914);
EOF
${GOTREE} generate caterpillartree --seed 10 > result
diff -q -b expected result
rm -f expected result
echo "->gotree generate uniformtree"
cat > expected <<EOF
(Tip5:0.08184535681853511,Tip0:0.30150414585026103,((Tip9:0.13492605122032592,Tip6:0.10309294031874587):0.01026581233891113,((Tip7:0.09740195047110385,(Tip8:0.027845992087631298,((Tip4:0.020616211789029896,Tip3:0.12467449897149811):0.1824683850061218,Tip2:0.19852695409349608):0.0440885662122905):0.1920960924280275):0.25879284932877245,Tip1:0.06718605070537677):0.1120177846434196):0.05817538156872999);
EOF
${GOTREE} generate uniformtree --seed 10 > result
diff -q -b expected result
rm -f expected result
echo "->gotree matrix"
cat > expected.brlen <<EOF
5
Tip0 0.000000000000 0.503664421046 0.566341541883 0.441187414330 0.462283254700
Tip1 0.503664421046 0.000000000000 0.551608647118 0.334576901471 0.447550359936
Tip2 0.566341541883 0.551608647118 0.000000000000 0.489131640402 0.145290710761
Tip3 0.441187414330 0.334576901471 0.489131640402 0.000000000000 0.385073353220
Tip4 0.462283254700 0.447550359936 0.145290710761 0.385073353220 0.000000000000
EOF
cat > expected.boot <<EOF
5
Tip0 0.000000000000 2.800000000000 2.800000000000 2.800000000000 2.800000000000
Tip1 2.800000000000 0.000000000000 3.600000000000 2.000000000000 3.600000000000
Tip2 2.800000000000 3.600000000000 0.000000000000 3.600000000000 2.000000000000
Tip3 2.800000000000 2.000000000000 3.600000000000 0.000000000000 3.600000000000
Tip4 2.800000000000 3.600000000000 2.000000000000 3.600000000000 0.000000000000
EOF
cat > expected.none <<EOF
5
Tip0 0.000000000000 3.000000000000 3.000000000000 3.000000000000 3.000000000000
Tip1 3.000000000000 0.000000000000 4.000000000000 2.000000000000 4.000000000000
Tip2 3.000000000000 4.000000000000 0.000000000000 4.000000000000 2.000000000000
Tip3 3.000000000000 2.000000000000 4.000000000000 0.000000000000 4.000000000000
Tip4 3.000000000000 4.000000000000 2.000000000000 4.000000000000 0.000000000000
EOF
echo "((Tip4:0.020616211789029896,Tip2:0.12467449897149811)0.8:0.1824683850061218,Tip0:0.25919865790518115,(Tip3:0.13604994737755394,Tip1:0.19852695409349608)0.8:0.04593880904706901);" > intree
${GOTREE} matrix -i intree > result
diff -q -b expected.brlen result
${GOTREE} matrix -i intree --metric boot > result
diff -q -b expected.boot result
${GOTREE} matrix -i intree --metric none > result
diff -q -b expected.none result
rm -f expected.brlen expected.boot expected.none result intree
echo "->gotree brlen setmin 1"
cat > expected <<EOF
((Tip4:1,(Tip7:1,Tip2:1):1):1,Tip0:1,((Tip8:1,(Tip9:1,Tip3:1):1):1,((Tip6:1,Tip5:1):1,Tip1:1):1):1);
EOF
${GOTREE} generate yuletree --seed 10 -l 10 | ${GOTREE} brlen setmin -l 1 > result
diff -q -b expected result
rm -f expected result
echo "->gotree brlen setmin 10"
cat > expected <<EOF
((Tip4:10,(Tip7:10,Tip2:10):10):10,Tip0:10,((Tip8:10,(Tip9:10,Tip3:10):10):10,((Tip6:10,Tip5:10):10,Tip1:10):10):10);
EOF
${GOTREE} generate yuletree --seed 10 -l 10 | ${GOTREE} brlen clear | ${GOTREE} brlen setmin -l 10 > result
diff -q -b expected result
rm -f expected result
echo "->gotree prune"
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)),Tip0);
EOF
${GOTREE} generate yuletree --seed 10 -l 20 | ${GOTREE} prune -i - -c <(${GOTREE} generate yuletree --seed 12 -l 10) | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result
echo "->gotree prune tipfile"
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)),Tip0);
EOF
cat > tipfile <<EOF
Tip6
Tip4
Tip0
Tip3
Tip9
Tip8
Tip2
Tip7
Tip5
Tip1
EOF
${GOTREE} generate yuletree --seed 10 -l 20 | ${GOTREE} prune -i - -f tipfile -r | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result tipfile
# echo "->gotree brlen setrand"
# cat > expected <<EOF
# ((Tip4:0.11181011331618643,(Tip7:0.21688356961855743,Tip2:0.21695890315161873):0.007486847792469759):0.02262551762264341,Tip0:0.07447903650558614,((Tip8:0.05414175839023796,(Tip9:0.34924246250387486,Tip3:0.023925115233614132):0.1890483249199916):0.03146499978313507,((Tip6:0.31897358778004786,Tip5:0.29071259678750266):0.04826059603128351,Tip1:0.02031669307269784):0.052025373286913534):0.011401847253594477);
# EOF
# ${GOTREE} generate yuletree --seed 10 | ${GOTREE} brlen setrand --seed 13 > result
# diff -q -b expected result
# rm -f expected result
echo "->gotree support setrand"
cat > expected <<EOF
((Tip4,(Tip7,Tip2)0.2550878763278657)0.6418716208549535,Tip0,((Tip8,(Tip9,Tip3)0.9581212767194948)0.24992593115716047,((Tip6,Tip5)0.2962112349523319,Tip1)0.2923644736644398)0.20284376043157062);
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} support setrand --seed 12 | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result
echo "->gotree rename"
cat > mapfile <<EOF
Tip0 Tax0
Tip1 Tax1
Tip2 Tax2
Tip3 Tax3
Tip4 Tax4
Tip5 Tax5
Tip6 Tax6
Tip7 Tax7
Tip8 Tax8
Tip9 Tax9
EOF
cat > expected <<EOF
((Tax4,(Tax7,Tax2)),Tax0,((Tax8,(Tax9,Tax3)),((Tax6,Tax5),Tax1)));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} rename -m mapfile | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result mapfile
echo "->gotree rename auto"
cat > mapfile <<EOF
Tip4 T0001
Tip7 T0002
Tip0 T0004
Tip9 T0006
Tip3 T0007
Tip1 T0010
Tip2 T0003
Tip8 T0005
Tip6 T0008
Tip5 T0009
EOF
cat > expected <<EOF
((T0001,(T0002,T0003)),T0004,((T0005,(T0006,T0007)),((T0008,T0009),T0010)));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} rename -a -m mapfile2 -l 5 | ${GOTREE} brlen clear > result
diff -q -b expected result
diff -q -b <(sort mapfile) <(sort mapfile2)
rm -f expected result mapfile mapfile2
echo "->gotree rename auto several trees"
cat > mapfile <<EOF
Tip4 T0001
Tip2 T0003
Tip8 T0005
Tip9 T0006
Tip1 T0010
Tip11 T0012
Tip14 T0014
Tip0 T0004
Tip3 T0007
Tip5 T0009
Tip12 T0011
Tip10 T0013
Tip13 T0015
Tip15 T0016
Tip7 T0002
Tip6 T0008
EOF
cat > input <<EOF
((Tip4,(Tip7,Tip2)),Tip0,((Tip8,(Tip9,Tip3)),((Tip6,Tip5),Tip1)));
((Tip12,Tip11),Tip0,((Tip4,(Tip7,Tip2)),((Tip8,(Tip9,Tip3)),(((Tip10,Tip6),(Tip14,Tip5)),(Tip13,Tip1)))));
((Tip12,Tip11),Tip0,((Tip4,(Tip7,(Tip15,Tip2))),((Tip8,(Tip9,Tip3)),(((Tip10,Tip6),(Tip14,Tip5)),(Tip13,Tip1)))));
EOF
cat > expected <<EOF
((T0001,(T0002,T0003)),T0004,((T0005,(T0006,T0007)),((T0008,T0009),T0010)));
((T0011,T0012),T0004,((T0001,(T0002,T0003)),((T0005,(T0006,T0007)),(((T0013,T0008),(T0014,T0009)),(T0015,T0010)))));
((T0011,T0012),T0004,((T0001,(T0002,(T0016,T0003))),((T0005,(T0006,T0007)),(((T0013,T0008),(T0014,T0009)),(T0015,T0010)))));
EOF
${GOTREE} rename -i input -a -m mapfile2 -l 5 | ${GOTREE} brlen clear > result
diff -q -b expected result
diff -q -b <(sort mapfile) <(sort mapfile2)
rm -f expected result mapfile mapfile2 input
echo "->gotree rename regexp"
cat > mapfile <<EOF
Tip4 Leaf4
Tip7 Leaf7
Tip0 Leaf0
Tip9 Leaf9
Tip3 Leaf3
Tip1 Leaf1
Tip2 Leaf2
Tip8 Leaf8
Tip6 Leaf6
Tip5 Leaf5
EOF
cat > expected <<EOF
((Leaf4,(Leaf7,Leaf2)),Leaf0,((Leaf8,(Leaf9,Leaf3)),((Leaf6,Leaf5),Leaf1)));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} rename --regexp 'Tip(\d+)' --replace 'Leaf$1' -m mapfile2 | ${GOTREE} brlen clear > result
diff -q -b expected result
diff -q -b <(sort mapfile) <(sort mapfile2)
rm -f expected result mapfile mapfile2
echo "->gotree reroot outgroup"
cat > expected <<EOF
((((Tip4,(Tip7,Tip2)),Tip0),((Tip6,Tip5),Tip1)),(Tip8,(Tip9,Tip3)));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} reroot outgroup Tip3 Tip8 Tip9 | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result
echo "->gotree reroot midpoint"
cat > expected <<EOF
(((Tip6,Tip5),Tip1),(((Tip4,(Tip7,Tip2)),Tip0),(Tip8,(Tip9,Tip3))));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} reroot midpoint | ${GOTREE} brlen clear> result
diff -q -b expected result
rm -f expected result
echo "->gotree resolve"
cat > expected <<EOF
((Tip4,(Tip7,Tip2)),(Tip3,(Tip9,Tip8)),(((Tip6,Tip5),Tip1),Tip0));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} collapse length -l 0.05 | ${GOTREE} resolve --seed 10 | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result
echo "->gotree resolve named"
cat > expected <<EOF
(T1:1,((T2:1,T3:1,N1:0)N1,T4:1,N2:0)N2:1,T5:1);
EOF
echo "(T1:1,((T2:1,T3:1)N1,T4:1)N2:1,T5:1);" | ${GOTREE} resolve named > result
diff -q -b expected result
rm -f expected result
echo "->gotree shuffletips"
cat > expected <<EOF
((Tip5,(Tip2,Tip3)),Tip7,((Tip8,(Tip4,Tip0)),((Tip6,Tip1),Tip9)));
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} shuffletips --seed 12 | ${GOTREE} brlen clear > result
diff -q -b expected result
rm -f expected result
# echo "->gotree subtree"
# cat > clade <<EOF
# clade:Tip2,Tip4,Tip7
# EOF
# cat > expected <<EOF
# (Tip4,(Tip7,Tip2))clade;
# EOF
# ${GOTREE} generate yuletree --seed 10 | ${GOTREE} annotate -m clade | ${GOTREE} subtree -n clade | ${GOTREE} brlen clear > result
# diff -q -b expected result
# rm -f expected result clade
echo "->gotree stats"
cat > expected <<EOF
tree nodes tips edges meanbrlen sumbrlen meansupport mediansupport rooted nbcherries colless sackin
0 18 10 17 0.14334492 2.43686361 NaN NaN unrooted 3 - -
EOF
cat > expected2 <<EOF
tree nodes tips edges meanbrlen sumbrlen meansupport mediansupport rooted nbcherries colless sackin
0 19 10 18 0.13538131 2.43686361 NaN NaN rooted 3 10 36
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} stats > result
diff -q -b expected result
${GOTREE} generate yuletree --seed 10 | ${GOTREE} reroot midpoint | ${GOTREE} stats > result
diff -q -b expected2 result
rm -f expected expected2 result
echo "->gotree stats edges"
cat > expected <<EOF
tree brid length support terminal depth topodepth rootdepth rightname comments leftname rightcomment leftcomment
0 0 0.1824683850061218 N/A false 1 3 -1 [] [] []
0 1 0.020616211789029896 N/A true 0 1 -1 Tip4 [] [] []
0 2 0.25879284932877245 N/A false 1 2 -1 [] [] []
0 3 0.09740195047110385 N/A true 0 1 -1 Tip7 [] [] []
0 4 0.015450672710905129 N/A true 0 1 -1 Tip2 [] [] []
0 5 0.25919865790518115 N/A true 0 1 -1 Tip0 [] [] []
0 6 0.04593880904706901 N/A false 1 4 -1 [] [] []
0 7 0.1920960924280275 N/A false 1 3 -1 [] [] []
0 8 0.027845992087631298 N/A true 0 1 -1 Tip8 [] [] []
0 9 0.01026581233891113 N/A false 1 2 -1 [] [] []
0 10 0.13492605122032592 N/A true 0 1 -1 Tip9 [] [] []
0 11 0.10309294031874587 N/A true 0 1 -1 Tip3 [] [] []
0 12 0.30150414585026103 N/A false 1 3 -1 [] [] []
0 13 0.05817538156872999 N/A false 1 2 -1 [] [] []
0 14 0.3779897840448691 N/A true 0 1 -1 Tip6 [] [] []
0 15 0.1120177846434196 N/A true 0 1 -1 Tip5 [] [] []
0 16 0.239082088939295 N/A true 0 1 -1 Tip1 [] [] []
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} stats edges > result
diff -q -b expected result
rm -f expected result
echo "->gotree stats edges /2 rooted"
cat > expected <<EOF
tree brid length support terminal depth topodepth rootdepth rightname comments leftname rightcomment leftcomment
0 0 N/A N/A false 1 2 1 [] [] []
0 1 N/A N/A true 0 1 2 1 [] [] []
0 2 N/A N/A true 0 1 2 2 [] [] []
0 3 N/A N/A false 1 2 1 [] [] []
0 4 N/A N/A true 0 1 2 3 [] [] []
0 5 N/A N/A false 1 2 2 [] [] []
0 6 N/A N/A true 0 1 3 4 [] [] []
0 7 N/A N/A true 0 1 3 5 [] [] []
EOF
echo "((1,2),(3,(4,5)));" | ${GOTREE} stats edges > result
diff -q -b expected result
rm -f expected result
echo "->gotree stats nodes"