test.sh

#!/usr/bin/env bash
########## 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 compute mutations --eems"
cat > input_align <<EOF
>A
A
>B
A
>AB
A
>C
A
>D
C
>CD
C
>ABCD
C
>E
T
>F
T
>EF
T
>G
T
>H
G
>GH
G
>EFGH
G
>ABCDEFGH
G
EOF

cat > input_tree <<EOF
(((A,B)AB,(C,D)CD)ABCD,((E,F)EF,(G,H)GH)EFGH)ABCDEFGH;
EOF

cat > expected <<EOF
Tree ID	Site	Parent Character	Child Character	Nb EEMs
0	0	G	T	2
0	0	C	A	2
0	0	G	C	1
EOF

${GOTREE} compute mutations -a input_align -i input_tree --eems >results
diff -q -b <(sort expected) <(sort results)
rm -f expected input_tree input_align results


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 matrix --avg"

cat > intree <<EOF
(1:1,2:0,(3:1,4:1):0);
(1:1,2:2,(3:2,4:2):1);
(1:3,2:2,(3:3,4:2):1);
(1:2,2:2,(3:0,4:1):1);
EOF

cat > expected <<EOF
4
1	0.000000000000	3.250000000000	4.000000000000	4.000000000000
2	3.250000000000	0.000000000000	3.750000000000	3.750000000000
3	4.000000000000	3.750000000000	0.000000000000	3.000000000000
4	4.000000000000	3.750000000000	3.000000000000	0.000000000000
EOF

${GOTREE} matrix -i intree --avg > result
diff -q -b expected result
rm -f expected intree result

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 brlen add"
cat > expected1 <<EOF
(A:11,(B:1,C:1):11);
EOF

cat > expected2 <<EOF
(A:10,(B,C):11);
EOF

cat > expected3 <<EOF
(A:11,(B:1,C:1):10);
EOF

echo "(A:10.0,(B,C):10);" | $GOTREE brlen add -l 1.0 > result
diff -q -b expected1 result
rm -f expected result

echo "(A:10.0,(B,C):10);" | $GOTREE brlen add -l 1.0 --external=false > result
diff -q -b expected2 result
rm -f expected result

echo "(A:10.0,(B,C):10);" | $GOTREE brlen add -l 1.0 --internal=false > result
diff -q -b expected3 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"
cat > expected <<EOF
tree	nid	nneigh	name	depth	comments	upnames	downnames
0	0	3		1	[]	-	Tip0
0	1	3		1	[]		Tip4
0	2	1	Tip4	0	[]		
0	3	3		1	[]		Tip7,Tip2
0	4	1	Tip7	0	[]		
0	5	1	Tip2	0	[]		
0	6	1	Tip0	0	[]		
0	7	3		2	[]		
0	8	3		1	[]		Tip8
0	9	1	Tip8	0	[]		
0	10	3		1	[]		Tip9,Tip3
0	11	1	Tip9	0	[]		
0	12	1	Tip3	0	[]		
0	13	3		1	[]		Tip1
0	14	3		1	[]		Tip6,Tip5
0	15	1	Tip6	0	[]		
0	16	1	Tip5	0	[]		
0	17	1	Tip1	0	[]		
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} stats nodes > result
diff -q -b expected result
rm -f expected result


echo "->gotree stats rooted"
cat > expected <<EOF
tree	rooted
0	unrooted
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} stats rooted > result
diff -q -b expected result
rm -f expected result


echo "->gotree stats splits"
cat > expected <<EOF
Tree	Tip9|Tip8|Tip7|Tip6|Tip5|Tip4|Tip3|Tip2|Tip1|Tip0
0	0010010100.
0	0000010000.
0	0010000100.
0	0010000000.
0	0000000100.
0	0000000001.
0	1101101010.
0	1100001000.
0	0100000000.
0	1000001000.
0	1000000000.
0	0000001000.
0	0001100010.
0	0001100000.
0	0001000000.
0	0000100000.
0	0000000010.
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} stats splits > result
diff -q -b expected result
rm -f expected result


echo "->gotree stats tips"
cat > expected <<EOF
tree	id	nneigh	name	ExternalBranch	RootToTip
0	2	1	Tip4	0.02061621	0.20308460
0	4	1	Tip7	0.09740195	0.53866318
0	5	1	Tip2	0.01545067	0.45671191
0	6	1	Tip0	0.25919866	0.25919866
0	9	1	Tip8	0.02784599	0.26588089
0	11	1	Tip9	0.13492605	0.38322677
0	12	1	Tip3	0.10309294	0.35139365
0	15	1	Tip6	0.37798978	0.78360812
0	16	1	Tip5	0.11201778	0.51763612
0	17	1	Tip1	0.23908209	0.58652504
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} stats tips > result
diff -q -b expected result
rm -f expected result

echo "->gotree labels"
cat > expected <<EOF
Tip4
Tip7
Tip2
Tip0
Tip8
Tip9
Tip3
Tip6
Tip5
Tip1
Tip5
Tip0
Tip6
Tip7
Tip4
Tip2
Tip8
Tip9
Tip3
Tip1
EOF
${GOTREE} generate yuletree --seed 10 -n 2 | ${GOTREE} labels > result
diff -q -b expected result
rm -f expected result


echo "->gotree internal labels"
cat > expected <<EOF
root
1
internal
2
polytomy
3
4
5
6
EOF

echo "(1,(2,(3,4,5,6)polytomy)internal)root;" | ${GOTREE} labels --internal > result
diff -q -b expected result
rm -f expected result

echo "->gotree unroot"
cat > expected <<EOF
((Tip9,Tip2),(Tip3,((((Tip8,Tip6),Tip5),Tip4),Tip1)),(Tip7,Tip0));
EOF
${GOTREE} generate yuletree -r --seed 10 | ${GOTREE} brlen clear | ${GOTREE} unroot > result
diff -q -b expected result
rm -f expected result

echo "->gotree draw text"
cat > expected <<EOF
          + Tip4                                  
+---------|                                       
|         |              +----- Tip7              
|         +--------------|                        
|                        + Tip2                   
|                                                 
|-------------- Tip0                              
|                                                 
|            +- Tip8                              
| +----------|                                    
| |          |+------- Tip9                       
| |          +|                                   
| |           +----- Tip3                         
+-|                                               
  |                    +--------------------- Tip6
  |                 +--|                          
  +-----------------|  +------ Tip5               
                    |                             
                    +------------- Tip1           
                                                  
EOF
${GOTREE} generate yuletree --seed 10 | ${GOTREE} draw text -w 50 > result
diff -q -b expected result
rm -f expected result

# echo "->gotree annotate"
# cat > inferred <<EOF
# (((((Hylobates_pileatus:0.23988592,(Pongo_pygmaeus_abelii:0.11809071,(Gorilla_gorilla_gorilla:0.13596645,(Homo_sapiens:0.11344407,Pan_troglodytes:0.11665038)0.62:0.02364476)0.78:0.04257513)0.93:0.15711475)0.56:0.03966791,(Macaca_sylvanus:0.06332916,(Macaca_fascicularis_fascicularis:0.07605049,(Macaca_mulatta:0.06998962,Macaca_fuscata:0)0.98:0.08492791)0.47:0.02236558)0.89:0.11208218)0.43:0.0477543,Saimiri_sciureus:0.25824985)0.71:0.14311537,(Tarsius_tarsier:0.62272677,Lemur_sp.:0.40249393)0.35:0)0.62:0.077084225,(Mus_musculus:0.4057381,Bos_taurus:0.65776307)0.62:0.077084225);
# EOF
# cat > annotated <<EOF
# ((((((((Gorilla_gorilla_gorilla[subspecies],Pan_troglodytes[species],Homo_sapiens[species])Homo/Pan/Gorilla_group[subfamily],Pongo_pygmaeus_abelii[species])Pongidae[family],Hylobates_pileatus[species])Hominoidea[superfamily],(Macaca_sylvanus[species],Macaca_fascicularis_fascicularis[subspecies],Macaca_fuscata[species],Macaca_mulatta[species])Macaca[genus])Catarrhini[parvorder],Saimiri_sciureus[species])Simiiformes[infraorder],Tarsius_tarsier[species])Haplorrhini[suborder],Lemur_sp.[species])Primates[order],Mus_musculus[species],Bos_taurus[species])Euarchontoglires[superorder];
# EOF
# cat > expected <<EOF
# (((((Hylobates_pileatus:0.23988592,(Pongo_pygmaeus_abelii:0.11809071,(Gorilla_gorilla_gorilla:0.13596645,(Homo_sapiens:0.11344407,Pan_troglodytes:0.11665038)0.62:0.02364476)Homo/Pan/Gorilla_group_0_3:0.04257513)Pongidae_0_4:0.15711475)Hominoidea_0_5:0.03966791,(Macaca_sylvanus:0.06332916,(Macaca_fascicularis_fascicularis:0.07605049,(Macaca_mulatta:0.06998962,Macaca_fuscata:0)0.98:0.08492791)Macaca_1_3:0.02236558)Macaca_0_4:0.11208218)Catarrhini_0_9:0.0477543,Saimiri_sciureus:0.25824985)Simiiformes_0_10:0.14311537,(Tarsius_tarsier:0.62272677,Lemur_sp.:0.40249393)0.35:0)Primates_0_12:0.077084225,(Mus_musculus:0.4057381,Bos_taurus:0.65776307)Primates_0_2:0.077084225);
# EOF
# ${GOTREE} annotate -i inferred -c annotated -o result
# diff -q -b expected result
# rm -f expected result annotated inferred


echo "->gotree reformat nexus"
cat > newick <<EOF
(fish, (frog, (snake, mouse)));
(fish, (snake, (frog, mouse)));
(fish, (mouse, (snake, frog)));
(mouse, (frog, (snake, fish)));
EOF
cat > expected <<EOF
#NEXUS
BEGIN TAXA;
 DIMENSIONS NTAX=4;
 TAXLABELS fish frog mouse snake;
END;
BEGIN TREES;
  TREE tree0 = (fish,(frog,(snake,mouse)));
  TREE tree1 = (fish,(snake,(frog,mouse)));
  TREE tree2 = (fish,(mouse,(snake,frog)));
  TREE tree3 = (mouse,(frog,(snake,fish)));
END;
EOF
${GOTREE} reformat nexus -i newick -f newick -o result
diff -q -b expected result
rm -f expected result newick

echo "->gotree reformat nexus --translate"
cat > newick <<EOF
(fish, (frog, (snake, mouse)));
(fish, (snake, (frog, mouse)));
(fish, (mouse, (snake, frog)));
(mouse, (frog, (snake, fish)));
EOF
cat > expected <<EOF
#NEXUS
BEGIN TAXA;
 DIMENSIONS NTAX=4;
 TAXLABELS fish frog mouse snake;
END;
BEGIN TREES;
  TRANSLATE
   0 fish
   1 frog
   3 mouse
   2 snake
  ;
  TREE tree0 = (0,(1,(2,3)));
  TREE tree1 = (0,(2,(1,3)));
  TREE tree2 = (0,(3,(2,1)));
  TREE tree3 = (3,(1,(2,0)));
END;
EOF
${GOTREE} reformat nexus --translate -i newick -f newick -o result
diff -q -b expected result
rm -f expected result newick

echo "->gotree reformat newick 0"
cat > newick <<EOF
(fish , (frog , (snake , mouse)));
(fish , (snake , (frog , mouse)));
(fish , (mouse , (snake , frog)));
(mouse , (frog , (snake , fish)));
EOF
cat > expected <<EOF
(fish,(frog,(snake,mouse)));
(fish,(snake,(frog,mouse)));
(fish,(mouse,(snake,frog)));
(mouse,(frog,(snake,fish)));
EOF
${GOTREE} reformat newick -i newick -f newick -o result
diff -q -b expected result
rm -f expected result newick


echo "->gotree reformat newick 1"
cat > nexus <<EOF
#NEXUS
BEGIN TAXA;
      DIMENSIONS NTAX=4;
      TaxLabels fish frog snake mouse;
END;

BEGIN CHARACTERS;
      Dimensions NChar=40;
      Format DataType=DNA;
      Matrix
        fish   ACATA GAGGG TACCT CTAAA
        frog   ACATA GAGGG TACCT CTAAC
        snake  ACATA GAGGG TACCT CTAAG
        mouse  ACATA GAGGG TACCT CTAAT

        fish   ACATA GAGGG TACCT CTAAG
        frog   CCATA GAGGG TACCT CTAAG
        snake  GCATA GAGGG TACCT CTAAG
        mouse  TCATA GAGGG TACCT CTAAG
;
END;

BEGIN TREES;
      Tree best=(fish, (frog, (snake, mouse)));
END;
EOF
cat > expected <<EOF
(fish,(frog,(snake,mouse)));
EOF
${GOTREE} reformat newick -i nexus -f nexus -o result
diff -q -b expected result
rm -f expected result nexus

echo "->gotree reformat nexus -> newick / translate"
cat > nexus <<EOF
#NEXUS
BEGIN TAXA;
      DIMENSIONS NTAX=4;
      TaxLabels fish frog snake mouse;
END;

BEGIN CHARACTERS;
      Dimensions NChar=40;
      Format DataType=DNA;
      Matrix
        fish   ACATA GAGGG TACCT CTAAA
        frog   ACATA GAGGG TACCT CTAAC
        snake  ACATA GAGGG TACCT CTAAG
        mouse  ACATA GAGGG TACCT CTAAT

        fish   ACATA GAGGG TACCT CTAAG
        frog   CCATA GAGGG TACCT CTAAG
        snake  GCATA GAGGG TACCT CTAAG
        mouse  TCATA GAGGG TACCT CTAAG
;
END;

BEGIN TREES;
      TRANSLATE
	0 fish,
	1 frog,
	2 snake,
	3 mouse;
      Tree best=(0, (1, (2, 3)));
END;
EOF
cat > expected <<EOF
(fish,(frog,(snake,mouse)));
EOF
${GOTREE} reformat newick -i nexus -f nexus -o result
diff -q -b expected result
rm -f expected result nexus

echo "->gotree reformat newick 2"
cat > nexus <<EOF
#NEXUS
[NEXUS COMMENT]
BEGIN TAXA;
      DIMENSIONS NTAX=4;[NEXUS COMMENT]
      [NEXUS COMMENT]
      TaxLabels fish frog snake mouse;[NEXUS COMMENT]
END;
[NEXUS COMMENT]
BEGIN CHARACTERS;
      [NEXUS COMMENT]
      Dimensions NChar=40;
      [NEXUS COMMENT]
      Format DataType=DNA;
      Matrix
        fish   ACATA GAGGG TACCT CTAAA
        frog   ACATA GAGGG TACCT CTAAC
        snake  ACATA GAGGG TACCT CTAAG
        mouse  ACATA GAGGG TACCT CTAAT

        fish   ACATA GAGGG TACCT CTAAG
        frog   CCATA GAGGG TACCT CTAAG
        snake  GCATA GAGGG TACCT CTAAG
        mouse  TCATA GAGGG TACCT CTAAG
;
[NEXUS COMMENT]
END;

BEGIN TREES;
      Tree best= [&R] (fish[COMMENT], (frog, (snake, mouse)));
END;
EOF
cat > expected <<EOF
(fish[COMMENT],(frog,(snake,mouse)));
EOF
${GOTREE} reformat newick -i nexus -f nexus -o result
diff -q -b expected result
rm -f expected result nexus

echo "->gotree reformat nexus->newick with translate"
cat > nexus <<EOF
#NEXUS
[NEXUS COMMENT]
BEGIN TREES;
      translate 1 fish
      , 2 frog
      , 3 snake,
      4 mouse;
      Tree best= [&R] (1[COMMENT], (2, (3, 4)));
END;
EOF
cat > expected <<EOF
(fish[COMMENT],(frog,(snake,mouse)));
EOF
${GOTREE} reformat newick -i nexus -f nexus -o result
diff -q -b expected result
rm -f expected result nexus

echo "->gotree reformat newick 3"
cat > nexus <<EOF
#NEXUS
BEGIN TAXA;
      TaxLabels fish frog mouse snake;
END;

BEGIN CHARACTERS;
      Dimensions NChar=40;
      Format DataType=DNA;
      Matrix
        fish   ACATA GAGGG TACCT CTAAA
        fish   ACATA GAGGG TACCT CTAAG

        frog   ACATA GAGGG TACCT CTAAC
        frog   CCATA GAGGG TACCT CTAAG

        snake  ACATA GAGGG TACCT CTAAG
        snake  GCATA GAGGG TACCT CTAAG

        mouse  ACATA GAGGG TACCT CTAAT
        mouse  TCATA GAGGG TACCT CTAAG
;
END;

BEGIN TREES;
      Tree best=(fish, (frog, (snake, mouse)));
END;
EOF
cat > expected <<EOF
(fish,(frog,(snake,mouse)));
EOF
${GOTREE} reformat newick -i nexus -f nexus -o result
diff -q -b expected result
rm -f expected result nexus

echo "->gotree acr acctran"
cat > tmp_states.txt <<EOF
1,A
2,A
3,B
4,B
5,A
6,B
7,B
8,A
9,A
10,A
11,A
EOF
cat > tmp_tree.txt <<EOF
(1,(2,((3,(4,5)),(6,((7,8),((9,10),11))))));
EOF
cat > expected <<EOF
(1[A],(2[A],((3[B],(4[B],5[A])[B])[B],(6[B],((7[B],8[A])[A],((9[A],10[A])[A],11[A])[A])[A])[B])[B])[A])[A];
EOF
${GOTREE} acr -i tmp_tree.txt --states tmp_states.txt --algo acctran -o result
diff -q -b expected result
rm -f expected result tmp_tree.txt tmp_states.txt

echo "->gotree acr downpass"
cat > tmp_states.txt <<EOF
t1,A
t2,A
t3,B
t4,B
t5,A
t6,B
t7,B
t8,A
t9,A
t10,A
t11,A
EOF
cat > tmp_tree.txt <<EOF
(t1,(t2,((t3,(t4,t5)),(t6,((t7,t8),((t9,t10),t11))))));
EOF
cat > expected <<EOF
(t1[A],(t2[A],((t3[B],(t4[B],t5[A])[A|B])[A|B],(t6[B],((t7[B],t8[A])[A|B],((t9[A],t10[A])[A],t11[A])[A])[A|B])[A|B])[A|B])[A])[A];
EOF
${GOTREE} acr -i tmp_tree.txt --states tmp_states.txt --algo downpass -o result
diff -q -b expected result
rm -f expected result tmp_tree.txt tmp_states.txt

echo "->gotree acr deltran"
cat > tmp_states.txt <<EOF
t1,A
t2,A
t3,B
t4,B
t5,A
t6,B
t7,B
t8,A
t9,A
t10,A
t11,A
EOF
cat > tmp_tree.txt <<EOF
(t1,(t2,((t3,(t4,t5)),(t6,((t7,t8),((t9,t10),t11))))));
EOF
cat > expected <<EOF
(t1[A],(t2[A],((t3[B],(t4[B],t5[A])[A])[A],(t6[B],((t7[B],t8[A])[A],((t9[A],t10[A])[A],t11[A])[A])[A])[A])[A])[A])[A];
EOF
${GOTREE} acr -i tmp_tree.txt --states tmp_states.txt --algo deltran -o result
diff -q -b expected result
rm -f expected result tmp_tree.txt tmp_states.txt


echo "->gotree asr acctran"
cat > tmp_states.txt <<EOF
11 2
1 AA
2 AA
3 CC
4 CC
5 AA
6 CC
7 CC
8 AA
9 AA
10 AA
11 AA
EOF
cat > tmp_tree.txt <<EOF
(1,(2,((3,(4,5)),(6,((7,8),((9,10),11))))));
EOF
cat > expected <<EOF
(1[AA],(2[AA],((3[CC],(4[CC],5[AA])[CC])[CC],(6[CC],((7[CC],8[AA])[AA],((9[AA],10[AA])[AA],11[AA])[AA])[AA])[CC])[CC])[AA])[AA];
EOF
${GOTREE} asr -i tmp_tree.txt -p -a tmp_states.txt --algo acctran -o result
diff -q -b expected result
rm -f expected result tmp_tree.txt tmp_states.txt

echo "->gotree asr downpass"
cat > tmp_states.txt <<EOF
11 4
t1 AAAT
t2 AAAT
t3 CCCT
t4 CCCT
t5 AAAT
t6 CCCT
t7 CCCT
t8 AAAT
t9 AAAT
t10 AAAT
t11 AAAT
EOF
cat > tmp_tree.txt <<EOF
(t1,(t2,((t3,(t4,t5)),(t6,((t7,t8),((t9,t10),t11))))));
EOF
cat > expected <<EOF
(t1[AAAT],(t2[AAAT],((t3[CCCT],(t4[CCCT],t5[AAAT])[{AC}{AC}{AC}T])[{AC}{AC}{AC}T],(t6[CCCT],((t7[CCCT],t8[AAAT])[{AC}{AC}{AC}T],((t9[AAAT],t10[AAAT])[AAAT],t11[AAAT])[AAAT])[{AC}{AC}{AC}T])[{AC}{AC}{AC}T])[{AC}{AC}{AC}T])[AAAT])[AAAT];
EOF
${GOTREE} asr -i tmp_tree.txt -p -a tmp_states.txt --algo downpass -o result
diff -q -b expected result
rm -f expected result tmp_tree.txt tmp_states.txt

echo "->gotree rotate sort"
cat > expected <<EOF
(6,(1,2),(5,(3,4)));
EOF
echo "((1,2),((3,4),5),6);" | ${GOTREE} rotate sort > result
diff -q -b expected result
rm -f expected result

echo "->gotree rotate sort 2"
cat > expected <<EOF
((6,7),(8,(9,10)),(5,((3,4),(1,(2,8)))));
EOF
echo "(((9,10),8),(((1,(2,8)),(3,4)),5),(6,7));" | ${GOTREE} rotate sort > result
diff -q -b expected result
rm -f expected result

#gotree generate all topologies
cat > expected <<EOF
(B,D,(E,(C,A)));
(B,D,(A,(E,C)));
(B,D,(C,(E,A)));
(D,(C,A),(E,B));
(B,(C,A),(E,D));
(D,(E,A),(C,B));
(A,D,(E,(C,B)));
(A,D,(B,(E,C)));
(A,D,(C,(E,B)));
(A,(C,B),(E,D));
(B,(E,A),(C,D));
(A,(E,B),(C,D));
(A,B,(E,(C,D)));
(A,B,(D,(E,C)));
(A,B,(C,(E,D)));
EOF
echo "(A,(B,D),(C,E));" | ${GOTREE} generate topologies -i - | ${GOTREE} rotate sort > result
diff -q -b expected result
rm -f expected result

#gotree round supports
echo "->gotree support round 3"
cat > expected <<EOF
(B,D,(E,(C,A)0.801)0.101);
EOF
cat > input <<EOF
(B,D,(E,(C,A)0.8009999999)0.100999999999999999);
EOF

${GOTREE} support round -i input -o output -p 3 > result
diff -q -b expected output
rm -f expected output input


#gotree round supports
echo "->gotree support round 8"
cat > expected <<EOF
(B,D,(E,(C,A)0.80000001)0.10000001);
EOF
cat > input <<EOF
(B,D,(E,(C,A)0.800000009999999)0.10000000999999999999999);
EOF

${GOTREE} support round -i input -o output -p 8 > result
diff -q -b expected output
rm -f expected output input

#gotree round lengths
echo "->gotree brlen round 3"
cat > expected <<EOF
(B,D,(E,(C,A):0.801):0.101);
EOF
cat > input <<EOF
(B,D,(E,(C,A):0.8009999999):0.100999999999999999);
EOF

${GOTREE} brlen round -i input -o output -p 3 > result
diff -q -b expected output
rm -f expected output input


#gotree round lengths
echo "->gotree brlen round 8"
cat > expected <<EOF
(B,D,(E,(C,A):0.80000001):0.10000001);
EOF
cat > input <<EOF
(B,D,(E,(C,A):0.800000009999999):0.10000000999999999999999);
EOF

${GOTREE} brlen round -i input -o output -p 8 > result
diff -q -b expected output
rm -f expected output input

#gotree brlen cut
echo "->gotree brlen cut"
cat > input <<EOF
(((1:0.1,2:0.1):0.5,((3:0.1,4:0.1):0.2,5:0.1):0.5):0.6,(6:0.1,7:0.1):0.5,(8:0.1,9:0.1):0.5);
EOF

cat > expected <<EOF
0	9	1,2,3,4,5,6,7,8,9
EOF
${GOTREE} brlen cut -i input  -l 1.0 | sort > output
diff -q -b expected output

cat > expected <<EOF
0	4	6,7,8,9
0	5	1,2,3,4,5
EOF
${GOTREE} brlen cut -i input -l 0.6 | sort > output
diff -q -b expected output

cat > expected <<EOF
0	2	1,2
0	2	6,7
0	2	8,9
0	3	3,4,5
EOF
${GOTREE} brlen cut -i input -l 0.5 | sort > output
diff -q -b expected output

cat > expected <<EOF
0	2	1,2
0	2	6,7
0	2	8,9
0	3	3,4,5
EOF
${GOTREE} brlen cut -i input -l 0.4 | sort > output
diff -q -b expected output

cat > expected <<EOF
0	2	1,2
0	2	6,7
0	2	8,9
0	3	3,4,5
EOF
${GOTREE} brlen cut -i input -l 0.3 | sort > output
diff -q -b expected output

cat > expected <<EOF
0	1	5
0	2	1,2
0	2	3,4
0	2	6,7
0	2	8,9
EOF
${GOTREE} brlen cut -i input -l 0.2 | sort > output
diff -q -b expected output

cat > expected <<EOF
0	1	1
0	1	2
0	1	3
0	1	4
0	1	5
0	1	6
0	1	7
0	1	8
0	1	9
EOF
${GOTREE} brlen cut -i input -l 0.1 | sort > output
diff -q -b expected output

cat > expected <<EOF
0	1	1
0	1	2
0	1	3
0	1	4
0	1	5
0	1	6
0	1	7
0	1	8
0	1	9
EOF
${GOTREE} brlen cut -i input -l 0.0 | sort > output
diff -q -b expected output

rm -f expected output input expected


#gotree brlen cut
echo "->gotree brlen cut / 2"
#
# 1--0.1------       ---0.2-----6
#             |     |
#             |-0.2-|
# 2-0.1-      |     |      -0.1-4
#       |-0.1-       -0.1-|
# 3-0.1-                   -0.1-5
#
cat > input <<EOF
((1:0.1,(2:0.1,3:0.1):0.1):0.2,(4:0.1,5:0.1):0.1,6:0.2);
EOF

cat > expected <<EOF
0	1	6
0	2	4,5
0	3	1,2,3
EOF
${GOTREE} brlen cut -i input  -l 0.2 | sort > output
diff -q -b expected output

rm -f expected output input

#gotree repopulate
echo "->gotree repopulate / 1"
cat > input <<EOF
(Tip4:0.1,Tip0:0.1,(Tip3:0.1,(Tip2:0.2,Tip1:0.2)0.8:0.3)0.9:0.4);
EOF
cat > id_groups <<EOF
Tip2,Tip5,Tip6,Tip7
Tip4,Tip8
EOF

cat > expected <<EOF
((Tip8:0,Tip4:0):0.1,Tip0:0.1,(Tip3:0.1,((Tip5:0,Tip2:0,Tip6:0,Tip7:0):0.2,Tip1:0.2)0.8:0.3)0.9:0.4);
EOF

cat > expectedcompare <<EOF
tree	reference	common	compared
0	0	4	0
EOF

${GOTREE} repopulate -i input -g id_groups -o output
${GOTREE} compare trees -i output -c expected > outputcompare
diff -q -b expectedcompare outputcompare
# Compare all branches with lengths, etc.
${GOTREE} compare edges -i output -c expected | tail -n+2 | awk -F "\t" '{if($3!=$15){exit 1};if($10!="true"){exit 1};if($9!=$14){exit 1}}'

rm -f expected output input outputcompare expectedcompare id_groups

#gotree repopulate
echo "->gotree repopulate / 2"
cat > input <<EOF
(Tip27,Tip0,(((Tip23,((Tip41,(Tip45,(Tip48,Tip25))),((Tip42,Tip30),((Tip35,Tip34),Tip12)))),(Tip16,Tip10)),((Tip11,Tip8),((((((((((Tip37,Tip20),Tip15),(Tip49,Tip14)),((Tip22,(Tip31,Tip19)),((Tip43,Tip28),(Tip46,Tip9)))),(Tip40,Tip7)),((Tip17,Tip13),(Tip47,Tip5))),((Tip18,Tip6),(Tip39,Tip4))),(Tip26,(Tip38,Tip3))),(Tip24,((Tip32,(Tip33,Tip29)),(Tip36,Tip2)))),((Tip44,Tip21),Tip1)))));
EOF
cat > id_groups <<EOF
Tip43,Tip100
Tip1,Tip101
Tip12,Tip102,Tip103,Tip104
Tip12,Tip105
Tip18,Tip106
Tip23
Tip1
Tip2
Tip3
Tip4
EOF

cat > expected <<EOF
(Tip27,Tip0,(((Tip23,((Tip41,(Tip45,(Tip48,Tip25))),((Tip42,Tip30),((Tip35,Tip34),(Tip12:0,Tip102:0,Tip103:0,Tip104:0,Tip105:0))))),(Tip16,Tip10)),((Tip11,Tip8),((((((((((Tip37,Tip20),Tip15),(Tip49,Tip14)),((Tip22,(Tip31,Tip19)),(((Tip43:0,Tip100:0),Tip28),(Tip46,Tip9)))),(Tip40,Tip7)),((Tip17,Tip13),(Tip47,Tip5))),(((Tip18:0,Tip106:0),Tip6),(Tip39,Tip4))),(Tip26,(Tip38,Tip3))),(Tip24,((Tip32,(Tip33,Tip29)),(Tip36,Tip2)))),((Tip44,Tip21),(Tip1:0,Tip101:0))))));
EOF

cat > expectedcompare <<EOF
tree	reference	common	compared
0	0	51	0
EOF

${GOTREE} repopulate -i input -g id_groups -o output
# Compare output topologies
${GOTREE} compare trees -i output -c expected > outputcompare
diff -q -b expectedcompare outputcompare
# Compare all branches with lengths, etc.
${GOTREE} compare edges -i output -c expected | tail -n+2 | awk -F "\t" '{if($3!=$15){exit 1};if($10!="true"){exit 1};if($9!=$14){exit 1}}'

rm -f expected output input outputcompare expectedcompare id_groups

#gotree generate startree
echo "->gotree generate startree"
cat > expected <<EOF
(Tip0,Tip1,Tip2,Tip3,Tip4,Tip5,Tip6,Tip7,Tip8,Tip9,Tip10);
(Tip0,Tip1,Tip2,Tip3,Tip4,Tip5,Tip6,Tip7,Tip8,Tip9,Tip10);
(Tip0,Tip1,Tip2,Tip3,Tip4,Tip5,Tip6,Tip7,Tip8,Tip9,Tip10);
EOF

${GOTREE} generate startree -l 11 -n 3 | ${GOTREE} brlen clear -o output
diff -q -b output expected

rm -f expected output

#gotree monophyletic
echo "->gotree stats monophyletic"
cat > input <<EOF
(6,7,((1,2),((3,4),5)));
(6,2,((1,7),((3,5),4)));
(6,7,((1,4),((3,2),5)));
EOF
cat > expected <<EOF
Tree	Monophyletic
0	true
1	true
2	false
EOF

cat > tipfile <<EOF
6
7
EOF

cat > expected2 <<EOF
Tree	Monophyletic
0	true
1	false
2	true
EOF

${GOTREE} stats monophyletic -i input -o result 3 4 5 
diff -q -b result expected

${GOTREE} stats monophyletic -i input -o result -l tipfile
diff -q -b result expected2

rm -f expected result input

#gotree monophyletic
echo "->gotree stats monophyletic /2"
cat > input <<EOF
(Tip68,Tip0,((((Tip51,(Tip71,Tip40)),Tip16),(Tip18,(Tip21,(Tip36,Tip9)))),(((((Tip31,((Tip63,((Tip79,Tip69),Tip32)),(((((Tip92,Tip58),Tip50),(Tip56,Tip41)),Tip33),((Tip96,Tip89),Tip15)))),(Tip70,(Tip90,(Tip93,Tip5)))),(((Tip49,Tip17),Tip7),(Tip27,(((Tip88,Tip57),(Tip97,Tip35)),((Tip53,Tip47),Tip3))))),(((((Tip25,(Tip87,(Tip99,Tip19))),(Tip59,(Tip61,Tip14))),(Tip30,((((Tip80,(Tip82,Tip66)),(Tip81,Tip46)),Tip43),Tip10))),(Tip37,Tip8)),((((Tip45,(Tip83,Tip44)),((Tip64,Tip60),Tip26)),Tip11),(((Tip78,(Tip84,Tip62)),Tip24),(Tip73,(Tip74,Tip2)))))),((((((Tip77,Tip65),(Tip94,Tip52)),Tip12),Tip6),((((Tip67,Tip54),(Tip85,Tip23)),(Tip76,Tip22)),(Tip34,(Tip38,Tip4)))),(((((Tip91,Tip75),Tip39),(Tip86,(Tip95,Tip29))),Tip13),((((Tip72,Tip55),(Tip98,Tip42)),(Tip48,Tip20)),(Tip28,Tip1)))))));
(Tip68,Tip0,((((Tip51,(Tip71,Tip40)),Tip16),(Tip18,(Tip21,(Tip36,Tip9)))),(((((Tip31,((Tip63,((Tip79,Tip69),Tip32)),(((((Tip92,Tip58),Tip49),(Tip56,Tip41)),Tip33),((Tip96,Tip89),Tip15)))),(Tip70,(Tip90,(Tip93,Tip5)))),(((Tip50,Tip17),Tip7),(Tip27,(((Tip88,Tip57),(Tip97,Tip35)),((Tip53,Tip47),Tip3))))),(((((Tip25,(Tip87,(Tip99,Tip19))),(Tip59,(Tip61,Tip14))),(Tip30,((((Tip80,(Tip82,Tip66)),(Tip81,Tip46)),Tip43),Tip10))),(Tip37,Tip8)),((((Tip45,(Tip83,Tip44)),((Tip64,Tip60),Tip26)),Tip11),(((Tip78,(Tip84,Tip62)),Tip24),(Tip73,(Tip74,Tip2)))))),((((((Tip77,Tip65),(Tip94,Tip52)),Tip12),Tip6),((((Tip67,Tip54),(Tip85,Tip23)),(Tip76,Tip22)),(Tip34,(Tip38,Tip4)))),(((((Tip91,Tip75),Tip39),(Tip86,(Tip95,Tip29))),Tip13),((((Tip72,Tip55),(Tip98,Tip42)),(Tip48,Tip20)),(Tip28,Tip1)))))));
(Tip68,Tip0,((((Tip51,(Tip71,Tip40)),Tip16),(Tip18,(Tip21,(Tip36,Tip9)))),(((((Tip31,((Tip63,((Tip79,Tip69),Tip32)),(((((Tip92,Tip58),Tip50),(Tip56,Tip41)),Tip33),((Tip96,Tip89),Tip15)))),(Tip70,(Tip90,(Tip93,Tip5)))),(((Tip1,Tip17),Tip7),(Tip27,(((Tip88,Tip57),(Tip97,Tip35)),((Tip53,Tip47),Tip3))))),(((((Tip25,(Tip87,(Tip99,Tip19))),(Tip59,(Tip61,Tip14))),(Tip30,((((Tip80,(Tip82,Tip66)),(Tip81,Tip46)),Tip43),Tip10))),(Tip37,Tip8)),((((Tip45,(Tip83,Tip44)),((Tip64,Tip60),Tip26)),Tip11),(((Tip78,(Tip84,Tip62)),Tip24),(Tip73,(Tip74,Tip2)))))),((((((Tip77,Tip65),(Tip94,Tip52)),Tip12),Tip6),((((Tip67,Tip54),(Tip85,Tip23)),(Tip76,Tip22)),(Tip34,(Tip38,Tip4)))),(((((Tip91,Tip75),Tip39),(Tip86,(Tip95,Tip29))),Tip13),((((Tip72,Tip55),(Tip98,Tip42)),(Tip48,Tip20)),(Tip28,Tip49)))))));
EOF
cat > expected <<EOF
Tree	Monophyletic
0	true
1	true
2	false
EOF

cat > tipfile <<EOF
Tip7
Tip49
Tip17
Tip27
Tip3
Tip53
Tip47
Tip88
Tip57
Tip97
Tip35
Tip70
Tip90
Tip93
Tip5
Tip31
Tip63
Tip32
Tip79
Tip69
Tip15
Tip96
Tip89
Tip33
Tip56
Tip41
Tip50
Tip92
Tip58
EOF


${GOTREE} stats monophyletic -i input -o result -l tipfile
diff -q -b result expected

rm -rf tipfile input expected result

echo "->gotree stats monophyletic rooted /1"
cat > input <<EOF
(((((Tip30,(((Tip69,Tip52),(Tip57,Tip50)),(Tip66,Tip28))),(Tip54,Tip3)),(Tip5,(((Tip60,Tip10),((Tip39,Tip12),(Tip59,(Tip82,(Tip86,Tip9))))),Tip2))),(((Tip11,(((Tip83,(Tip94,Tip24)),Tip22),(Tip38,(((Tip74,Tip49),(Tip58,(Tip63,Tip46))),Tip6)))),((Tip68,((Tip92,(Tip98,Tip85)),Tip17)),(((Tip88,(Tip99,Tip73)),Tip42),(Tip77,Tip4)))),(((((Tip72,Tip37),Tip34),(Tip75,Tip18)),(((Tip84,Tip70),Tip19),(((Tip90,Tip23),Tip20),(((Tip93,Tip65),(Tip81,Tip31)),(Tip78,Tip14))))),((Tip21,((Tip87,Tip47),Tip16)),((Tip51,Tip25),((Tip43,Tip26),Tip1)))))),(((Tip36,(Tip53,(Tip61,Tip15))),((Tip35,(Tip97,Tip33)),((Tip96,Tip40),((Tip48,(Tip55,(Tip71,Tip45))),((Tip79,Tip76),Tip7))))),(Tip8,(((Tip41,(((Tip91,Tip62),((Tip89,Tip80),Tip56)),(Tip64,((Tip95,Tip67),Tip29)))),(Tip44,Tip13)),((Tip32,Tip27),Tip0)))));
EOF
cat > expected <<EOF
Tree	Monophyletic
0	true
EOF

cat > tipfile <<EOF
Tip36
Tip53
Tip61
Tip15
Tip35
Tip97
Tip33
Tip96
Tip40
Tip7
Tip79
Tip76
Tip48
Tip55
Tip71
Tip45
EOF


${GOTREE} stats monophyletic -i input -o result -l tipfile
diff -q -b result expected

rm -rf tipfile input expected result

echo "->gotree stats monophyletic rooted /2"
cat > input <<EOF
(((((Tip30,(((Tip69,Tip52),(Tip57,Tip50)),(Tip66,Tip28))),(Tip54,Tip3)),(Tip5,(((Tip60,Tip10),((Tip39,Tip12),(Tip59,(Tip82,(Tip86,Tip9))))),Tip2))),(((Tip11,(((Tip83,(Tip94,Tip24)),Tip22),(Tip38,(((Tip74,Tip49),(Tip58,(Tip63,Tip46))),Tip6)))),((Tip68,((Tip92,(Tip98,Tip85)),Tip17)),(((Tip88,(Tip99,Tip73)),Tip42),(Tip77,Tip4)))),(((((Tip72,Tip37),Tip34),(Tip75,Tip18)),(((Tip84,Tip70),Tip19),(((Tip90,Tip23),Tip20),(((Tip93,Tip65),(Tip81,Tip31)),(Tip78,Tip14))))),((Tip21,((Tip87,Tip47),Tip16)),((Tip51,Tip25),((Tip43,Tip26),Tip1)))))),(((Tip36,(Tip53,(Tip61,Tip15))),((Tip35,(Tip97,Tip33)),((Tip96,Tip40),((Tip48,(Tip55,(Tip71,Tip45))),((Tip79,Tip76),Tip7))))),(Tip8,(((Tip41,(((Tip91,Tip62),((Tip89,Tip80),Tip56)),(Tip64,((Tip95,Tip67),Tip29)))),(Tip44,Tip13)),((Tip32,Tip27),Tip0)))));
EOF
cat > expected <<EOF
Tree	Monophyletic
0	false
EOF

# Missing Tip7 to be a monophyletic group
cat > tipfile <<EOF
Tip36
Tip53
Tip61
Tip15
Tip35
Tip97
Tip33
Tip96
Tip40
Tip79
Tip76
Tip48
Tip55
Tip71
Tip45
EOF


${GOTREE} stats monophyletic -i input -o result -l tipfile
diff -q -b result expected

rm -rf tipfile input expected result


echo "->gotree stats monophyletic rooted /3"
cat > input <<EOF
(((((Tip30,(((Tip69,Tip52),(Tip57,Tip50)),(Tip66,Tip28))),(Tip54,Tip3)),(Tip5,(((Tip60,Tip10),((Tip39,Tip12),(Tip59,(Tip82,(Tip86,Tip9))))),Tip2))),(((Tip11,(((Tip83,(Tip94,Tip24)),Tip22),(Tip38,(((Tip74,Tip49),(Tip58,(Tip63,Tip46))),Tip6)))),((Tip68,((Tip92,(Tip98,Tip85)),Tip17)),(((Tip88,(Tip99,Tip73)),Tip42),(Tip77,Tip4)))),(((((Tip72,Tip37),Tip34),(Tip75,Tip18)),(((Tip84,Tip70),Tip19),(((Tip90,Tip23),Tip20),(((Tip93,Tip65),(Tip81,Tip31)),(Tip78,Tip14))))),((Tip21,((Tip87,Tip47),Tip16)),((Tip51,Tip25),((Tip43,Tip26),Tip1)))))),(((Tip36,(Tip53,(Tip61,Tip15))),((Tip35,(Tip97,Tip33)),((Tip96,Tip40),((Tip48,(Tip55,(Tip71,Tip45))),((Tip79,Tip76),Tip7))))),(Tip8,(((Tip41,(((Tip91,Tip62),((Tip89,Tip80),Tip56)),(Tip64,((Tip95,Tip67),Tip29)))),(Tip44,Tip13)),((Tip32,Tip27),Tip0)))));
EOF

cat > expected <<EOF
Tree	Monophyletic
0	false
EOF

cat > expected2 <<EOF
Tree	Monophyletic
0	true
EOF

cat > tipfile <<EOF
Tip36
Tip53
Tip61
Tip15
Tip35
Tip97
Tip33
Tip96
Tip40
Tip7
Tip79
Tip76
Tip48
Tip55
Tip71
Tip45
Tip8
Tip0
Tip32
Tip27
Tip44
Tip13
Tip41
Tip64
Tip29
Tip95
Tip67
Tip91
Tip62
Tip56
Tip89
Tip80
Tip54
Tip3
Tip30
Tip66
Tip28
Tip69
Tip52
Tip57
Tip50
Tip5
Tip2
Tip60
Tip10
Tip39
Tip12
Tip59
Tip82
Tip86
Tip9
EOF

${GOTREE} stats monophyletic -i input -o result -l tipfile
diff -q -b result expected

${GOTREE} unroot -i input | ${GOTREE} stats monophyletic -o result -l tipfile
diff -q -b result expected2

rm -rf tipfile input expected expected2 result


echo "->gotree graft"
cat > input.t1 <<EOF
(l1:0.1,l2:0.2,l3:0.3);
EOF
cat > input.t2 <<EOF
(l4:0.1,l5:0.2,l6:0.3);
EOF

cat > expected <<EOF
((l4:0.1,l5:0.2,l6:0.3):0.1,l2:0.2,l3:0.3);
EOF

${GOTREE} graft -i input.t1 -c input.t2 -l l1 -o result
diff -q -b result expected

rm -rf input.t1 input.t2 expected result


echo "->gotree collapse clade"
cat > input.t1 <<EOF
((l4:0.1,l5:0.2,l6:0.3):0.1,l2:0.2,l3:0.3);
EOF

cat > input.t2 <<EOF
((l4:0.1,(l5:0.2,l7:0.4):0.5,l6:0.3):0.1,l2:0.2,l3:0.3);
EOF

cat > input.tips <<EOF
l4
l5
EOF

cat > expected <<EOF
(l1:0.1,l2:0.2,l3:0.3);
EOF

cat > expected.clade <<EOF
(l4:0.1,l5:0.2,l6:0.3);
EOF


cat > expected2 <<EOF
((l1:0.1,l5:0.2,l6:0.3):0.1,l2:0.2,l3:0.3);
EOF

cat > expected2.clade <<EOF
l4;
EOF


cat > expected3 <<EOF
(l1:0.1,l2:0.2,l3:0.3);
EOF

cat > expected3.clade <<EOF
(l4:0.1,(l5:0.2,l7:0.4):0.5,l6:0.3);
EOF

${GOTREE} collapse clade -i input.t1 -l input.tips -n l1 -c result.clade -o result
diff -q -b result expected
diff -q -b result.clade expected.clade

${GOTREE} collapse clade -i input.t1 -n l1 -c result.clade -o result  l4 l5 l6
diff -q -b result expected
diff -q -b result.clade expected.clade

${GOTREE} collapse clade -i input.t1 -n l1 -c result.clade -o result l4
diff -q -b result expected2
diff -q -b result.clade expected2.clade

${GOTREE} collapse clade -i input.t2 -n l1 -c result.clade  -o result l5 l4
diff -q -b result expected3
diff -q -b result.clade expected3.clade

rm -rf input.t1 input.tips input.t2 expected expected2 expected3 result result.clade expected3.clade expected2.clade expected.clade


echo "->gotree ltt"
cat > expected <<EOF
0	0.000000	2
0	1.000000	3
0	2.000000	4
0	3.000000	6
0	3.500000	7
0	4.000000	8
0	5.000000	0
EOF

echo "(((A:1,B:1):1,C:2):3,(D:4,(E:3,((F:1.5,G:1.5):0.5,H:2):1):1):1);" | $GOTREE ltt > result
diff -q -b expected result
rm -f expected result

echo "->gotree ltt with dates"
cat > expected <<EOF
0	2019.000000	2
0	2020.000000	3
0	2021.000000	4
0	2022.000000	6
0	2022.500000	7
0	2023.000000	8
0	2024.000000	0
EOF
echo '(((A[&date="2024"]:1,B[&date="2024"]:1)[&date="2023"]:1,C[&date="2024"]:2)[&date="2022"]:3,(D[&date="2024"]:4,(E[&date="2024"]:3,((F[&date="2024"]:1.5,G[&date="2024"]:1.5)[&date="2022.5"]:0.5,H[&date="2024"]:2)[&date="2022"]:1)[&date="2021"]:1)[&date="2020"]:1)[&date="2019"];' | $GOTREE ltt > result
diff -q -b expected result
rm -f expected result