Commit bbfbc4c1 authored by Damien Leroux's avatar Damien Leroux
Browse files

Added some simulated data and a hidden output in spell-marker to double-check the results.

parent 5303d460
......@@ -18,15 +18,48 @@
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......@@ -82,8 +115,8 @@
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......@@ -268,10 +301,10 @@
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......@@ -702,11 +753,18 @@
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......@@ -731,7 +789,7 @@
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......@@ -758,7 +816,8 @@
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2016-04-06 17:44:39.673660
POP A 1
POP F1 1
POP C 1
POP B 1
POP F1C 1
POP F2 100
POP F2C 100
QTL 140.28 50.2
trait t1 qtl [('M_1_18', 140.28), ('M_1_8', 50.2)] effect [{'a': 1.0, 'c': -1.0}, {'a': 1.0, 'c': -1.0}] epistasis {} noise 1.0 0.0 2.0
trait t1 qtl [('M_1_18', 140.28), ('M_1_8', 50.2)] effect [{'a': 1.0, 'b': 0.0}, {'a': 1.0, 'b': 0.0}] epistasis {} noise 1.0 0.0 1.0
*ch1 18 M_1_1 2.76 M_1_2 6.45 M_1_3 4.56 M_1_4 14.54 M_1_5 1.06 M_1_6 14.65 M_1_7 19.63 M_1_9 0.04 M_1_10 6.61 M_1_11 4.22 M_1_12 19.54 M_1_13 2.03 M_1_14 20.58 M_1_15 4.92 M_1_16 0.82 M_1_17 21.78 M_1_19 5.81 M_1_20
generation;individual;mother;father
A;1;0;0
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F1C;5;1;3
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F2;8;4;4
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F2C;192;5;5
F2C;193;5;5
F2C;194;5;5
F2C;195;5;5
F2C;196;5;5
F2C;197;5;5
F2C;198;5;5
F2C;199;5;5
F2C;200;5;5
F2C;201;5;5
F2C;202;5;5
F2C;203;5;5
F2C;204;5;5
F2C;205;5;5
{
name: '100',
map: '100.map',
pedigree: '100.ped',
marker_observation_formats: [
'ABHCD': 'format-ABHCD.xml'
},
marker_observations: [
{
generation: 'F2',
format: 'ABHCD',
file: '100_F2.gen',
},
{
generation: 'F2C',
format: 'ABHCD',
file: '100_F2C.gen',
},
],
working_directory: '.',
multithread: 'auto',
sge: 'no',
}
data type F2
100 20 0 0
*M_1_1 ABHHBAHHAHHHHBBBHHHHABAHBBBHBAHABHAHHBBHBAHAHHHBBHHHHHHHAAHAHBHAHAHABHHBBBAHAHBHAHHHBBBHHBHHHHHHHBHA
*M_1_2 HBHHBAHHAHHHHBBBHBAHHBAHBBBHBAHABHAHHBBHBAHAHHHBHBHHHHHHAAAAHBHAHAHABHHBBBAHABBHAHHHBBBHHBHHHHHHHBHA
*M_1_3 HBBHBAHHAHHHHBBBHHAHHBAHBBBABAHABAAHHBBHBAHAHHHBHBHHHBHHAAAAHBHAHAHABHHHBBAHAHBHAHHHBBBHHBHAHHHBHBHA
*M_1_4 HBBHBAHHAHHHHBBBHHAHHBABBBBABAHABAAHHBBHBAHAHHHBHBHHABHHAAAAHBHAHAHABAHHBBAHAHHHABHHHBHHABBAHHHBHBHA
*M_1_5 HBHHBAHHAHHHABBHHHAHHBABHBBAHAHABHAHHBBHHAHABHBHHBHAAAHHAAAHHBHAHAHABAHHBBAHAHHHABHBHBHHHBBAHHHBHBAA
*M_1_6 HBHHBAHHAHHHABBHHHAHHHABHBBAHAHABHAHHBBHHAHABHBHHBHAAAHHAAABHBHAHAHABAHHBBAHHHHHABHBHBHHHBBAHHHBHBAA
*M_1_7 HHHHBHHHABHHAHBHHBAHHHHHHBBAAAHAHHHHHBBBAAHAHHBHHBAAAHAHAAABHBHAHAHABAAHHBAABHHHABHHBBHHHBHAAHHBHBAA
*M_1_8 ABBHBHHHABHHABBHHBAHHHHHABBAAAHABHHHHBBHAAHABHBHHHAAAHAHAAABHBHAHAHABHBHHBAABBHHABHHBBAHHBHAAHHBHBAA
*M_1_9 ABBHBHHHABHHAHBHHBHAHHHHABBHAAHHHHHHHBBAHAHHBHHHHHAAAHAHAAHBABHHHAHABHBHHBAAHBHHABHABHHHHBHAAHHAABAH
*M_1_10 ABBHBHHHABHHAHBHHBHAHHHHABBHAAHHHHHHHBBAHAHHBHHHHHAAAHAHAAHBABHHHAHABHBHHBAAHBHHABHABHHHHBHAAHHAABAH
*M_1_11 HBBHBHHHABHHABBHHBHAHAHHABHHAAHHHHHBHBBAHAHHBHHBHHAAAHAHAAHBABHHHAHHBHBHHBAAHBHHABHAHHHHHBHAHHHAAHHH
*M_1_12 HBBHBHHHABBHHBBHHHHAHAHHABAHAAHHHHHBHBBAAAHHBHHBHHAAAHAHAAHBABHHHAHHBHBBBBAAHBHHABHAHAHHHBHAAAHAAHHH
*M_1_13 HBHHBHHHHBBHHBHHBAHHHAHHABAHHHHHHHHBHBBAAAAHBHHBHHAHAHABAAHHAHHAHAHHBBBBBBAHHHHHHBHHHHHHHBHHHAHHAHHA
*M_1_14 HBHHBHHHHBBAHBHHBAHHHAHHABAHHHHHHHHHHBBAAAAHBHHBHHAAAHABAAHHAHHAHAHHBBBBBBAHHHHHHBHHHHHHHBHHHAHHAHHA
*M_1_15 ABHHBAHHHBBAABABBHAHBAHAAHABHHHHHBHBBHBHHAAHHHHBHAAABAAHAAHHHHHHHAHBBBABBBHBHHHHBBHBHHHBBBAHHAHBHAHA
*M_1_16 ABHHHAHHHBBAABABBHAHBABAAHABHHHHHBHBBHBHHAAHHHHBHAAABAAHAAHBHHHHHAHBHBABBBHBHHHHBBHBHHHBBBABHAHHHAAA
*M_1_17 ABHHHAHHHBBAABABBHAHBABAAHABHHHHHBHBBHBHHAAHHHHBHAAABAAHAAHBHHHHHAHBHBABBBHBAHHHBBHBHHHBBBABHAHHHAAA
*M_1_18 HBAHHAHHHBBAABAHBHHHBHHAAHABHABHHBHBHHBHHAAABHHBAHAABAAAAHABHHAHHAHHHAABBBHHAAHHBBHBHHHBHBABHABHHAAA
*M_1_19 BBAHHAHHHBBAABAHBHHHBHHAABABHABHHBHBHHBHHAAABHHBAHAABAAAAHABHHAHHAHHHAABBBHHHAHHBBHBAHHBHBABHABABAHA
*M_1_20 HBAHHAHHABBAABAHBHHHBHHAABHBHABHHHHBHHBHHAAABBHBAHAABAAAAHHBHHABHAHHHAHBBBHHHAHHBBHBAAHBHBABHABABHAH
*t1 3.51713931945 1.0246701196 0.953090800053 2.57999612702 2.47728407603 3.03757885822 2.18937007971 2.8940202609 3.51898482156 -0.17285578766 0.574599325833 4.16070044451 5.4320984649 -1.23796912122 3.3491920138 2.89152013733 -0.164407238649 0.144043123652 3.57902586997 1.94638300867 0.86868871079 1.92961525797 2.10055356177 3.82628594012 3.626261374 0.713374567494 3.16572555659 1.3319504318 2.95440204583 4.9435015301 0.0327408769344 4.79522302049 0.462342629727 -0.169902448399 1.11436824923 -0.517979243726 3.90865670254 -0.452578013059 -0.205810387479 0.255314026987 3.11119790883 4.06039276039 2.27231562298 5.24814998136 -0.398855281502 3.25061756463 0.604496286219 0.613148314873 1.81418648361 2.31173422355 4.83882672325 5.38505485478 2.25291168242 3.00144531156 3.21007794593 3.96330191575 4.88311030165 3.42471880923 3.70513715347 0.266613510032 1.86932276559 2.76831445039 1.62061963331 3.70920141572 0.963016496162 3.65096776873 2.03182907949 3.99115925789 1.19027380859 2.44842913403 3.35590074159 0.546795302528 2.15273105428 0.907865954528 2.57376614879 3.15961398368 0.718367280892 2.47820425545 1.93971864714 2.3624013057 2.90609181534 1.06515378915 0.791235734501 1.94441631704 0.807413775663 1.01031988636 2.58203032493 0.925439169823 2.32127168613 1.11534653575 2.91747499899 1.84524938489 0.483318000136 3.06740837281 0.443629665309 0.201651062031 2.73963175743 2.10383069493 4.63887520359 3.04492191481
data type F2C
100 20 0 0
*M_1_1 HHHHHHBAHBBHBBABHHAAHHAHHHAHHHABHAHAAHAHAHHHBHABHHHAAHABHHBHBBHAHHBHBHAHBHHBBBHHBBBHAHHBBAAHAHHAHHHH
*M_1_2 HHHHHHBAHBBHHBABHHAAHHHHBHAHHHABHAHAAHAHHHHHBHABHHHAAAAHHHBHBBHHHHBHBHAHBHHBBBHHBBBHAHHBBAAHAHHAAHHB
*M_1_3 HHHHHHBAHHBHHBAHHHAAAHAHBAAHHHABHAHAAHAHHHHBBHABHHBHAAAHAHBHBBAHHHBHBHAHBHHBBBHHBBBHABHBBAAHAHHAAHHB
*M_1_4 HHHHHHHAAHBHHBAHHHAAAHABBAAHHHABHAHAAHAHHHHBBBABHBBHAAAHAHBHHHAHHHHHBHAHBHHBHHHHBBBHABBBBAAAAAHAAHHB
*M_1_5 HHHHHHBHHHBHHBAHHAHAABABHAAABHABHAAAAHAHHHHBBHABHHBHAAAHAHBHHHAHHAAHBHABBHHBAHBHHABAABBHBAAHAABHAHHB
*M_1_6 HHHHHHBHHHBHHBAHHAHAABABHAAABHABHAAAAHAHHHHBBHABHHBHAAAHAHBHHHAHHAAHBHABBHHBAHBHHABAHBBHBAAHAABHAHHB
*M_1_7 HHBHABBHHHBHHHAHHHHAAHABHAAHBHABHAAAAHAHHHHBHHABHBBHAAAAAHBABHAHHHAHBHABBHHBAABHHAHAHBHHBAAHAABHHAAB
*M_1_8 HHHHABBHHHBHAHHHHHHAHHABHAAHBHABHAAAAHAHHHHBHHABHBBHAAAAAHBABHAHHHAABAABBHHHAABHHAHAHHHHBAAHAAHHBAAB
*M_1_9 HAHHHBHAAHBHAHHBHHHAHHHBHAAHBHABHAAAAHAHHABBHHABBBBHAAAAAAHABHHHHHAHBHHBBHAHAABHHAHAHHHHBAAHAAHHBAAB
*M_1_10 HAHHHBHAAHBHAHHBHHHAHHHBHAAHBHABHAAAAHAHHABBHHABBBBHAAAAAAHABHHHHHAHBHHBBHAHAABHHAHAHHHHBAAHAAHHBAAB
*M_1_11 HHHHHBHAAHBHAHHAHBHAHHABHAAABHHBHAAAHHAHHABBHHABBHBAAAAAAAHABHHAHBAHBHHBBAABHABHHAHHHHHHBAABAAHHHAAB
*M_1_12 HHHHHHHAAHBHAHHAHBHAHHHBHAAABHABHAHAHHAHHABBHHABBHBAAAAAAAHABHHAHBAHBHHBBHAHAHBHHAHHHHHHBAAHAAHHHAAB
*M_1_13 HHHAHHAHBBAHAHAABBHAHHHBHAAABAABBAHAHHAHHHBHHAAHBHBAAHAHABHABHHAABABBHHHBHHHAHBHHAAHAHAHBAAHAAHHHHAB
*M_1_14 HHHAHHAHBHAHAHAABBHAHHHBHAAABAABHAHAHHHHHHBAHAAHBHBAAHAHABHHBHHAABABBHHHBHHHAHBHHAAHAHAHBAAHAAHHHAAB
*M_1_15 BHHAHHABBBAHAHAHHBHABHBHHAHAHAABHAHHHAHAHHHAHAAHBHBAHHHHAHHHHHHHAHABBAHHHHHHAHHHHHAHABAHHAABAHBBHAAB
*M_1_16 BHHAHHAHBBAHAHAHHBHABHBHHAHAHAABHAHHHAAAHHHHHAAHBHBAHHHHAHHHHHHHAHABBAHHHHHHAHHHHHAHABAHBAABAHBBHAAB
*M_1_17 BHHAHHABBBAHAHAHHBHABHBHHAHAHAABHAHHHAAAHHHHHAAHBHBAHHHHHHHHHHHHAHABBAHHHHHHAHHHHHAHABAHBAABAHBBHAAB
*M_1_18 BHHAHHHBHBAHAHAHHBAAAHBHHAHAAHAHHAHHHAAAHHHHHHABBHBABHAAHAHAHAHHHHHHHABHHAAHAHHBHAHHHAHHBHHBAHBBHAAB
*M_1_19 BHHAHHHBHBAHAHHHHBAAAHBHAAHAAHAHHAAAHAAAHHAHHHABBHBABHAAHHHAHAHHBHHHHABHHAAHAHHBHAHHHAHHBHHBHHBBHAAB
*M_1_20 BABAHHHBHBAHHHHHHBAAAHBHAAHAAHABHAAAHAAAHHAHHHHBBHBABHAAAHHAHHAHBHHAHABHHAHHAHHBHHHHHHHBHHHBHHBBHAAB
*t1 -0.03114127484 1.12720167618 2.41912772327 5.19217796282 5.36601828558 -0.169895930883 -1.85399649347 -0.123836531561 0.676960409711 -6.85116539225 1.87812622886 1.27980009963 8.28036769918 -0.494560678295 0.0125945349779 -1.73624891611 -2.5652737215 -2.64457592105 2.80694428613 4.17143583664 3.44942671051 0.493069124658 0.329124415669 -3.76997128147 -1.06753541316 6.35990418217 0.195436052181 2.42228815527 -3.15501351389 2.69981041237 0.0417879336556 -3.38744311898 0.680661658566 3.94840080721 2.27098838458 1.18993131742 1.32658058963 1.06465056548 8.65541683047 -0.0684899193324 -0.010433509858 -0.363806969835 -1.04931889692 -0.150500243436 0.712671802285 1.11439752196 5.54734594329 -4.99176838072 -5.05512429144 -3.08884935967 0.286289316376 -0.997611395226 -1.30913891349 3.95357605539 3.30219063717 4.25435548782 0.712237624434 -2.48090876322 -0.727870281518 2.1292865654 -3.9049973463 -3.85047632705 2.40946219382 -0.714462994593 2.40537593085 -0.3801565466 1.23103907644 1.35984351267 2.0283834891 -0.0697765090769 -0.175461793253 -1.65196776577 2.96430964613 3.31650355381 5.04288154109 1.68407936073 4.50572481714 7.29204475458 -0.47271443205 -4.54132839875 0.851496871243 3.53528077645 -1.1185621408 4.35394710671 1.18250270213 2.02666923952 -2.67558779473 1.86948231605 -2.13222658604 2.16843567758 -0.668825730026 -1.65956023676 3.25387493172 1.14452649258 -2.69717534826 -2.69964323141 -3.92774452627 4.663784628 6.973890795 -5.51513416839
(cd ../../src && make -j) && \
#valgrind --leak-check=full \
#strace \
#gdb-7.6 --args \
valgrind \
../../src/spell-qtl \
-n multipop -wd tmp \
-bds design-F2.xml \
-gm micro.map -mos format-ABHCD.xml \
-p AB F2 micro_F2.phen -m F2:ABHCD micro_F2.gen \
-p AC F2C micro_F2C.phen -m F2C:ABHCD micro_F2C.gen \
connected \
step 1 -na -wd ./tmp \
skeleton auto 30 \
cofactor-detection none \
QTL-detection iQTLm \
-P 8 \
qtl-threshold-value trait1=1.85 \
spell-pedigree -p 100.ped
spell-marker -p 100.ped.ped-data -mos format-ABHCD.xml -m F2:ABHCD 100_F2.gen -m F2C:ABHCD 100_F2C.gen -n 100 -mt 8
spell-qtl -P auto -n test-2pop -wd /media/RAM/test-2pop -gm 100.map -p 100.popdata F2 100_F2.phen -p 100.popdata F2C 100_F2C.phen QTL-detection iQTLm cofactor-detection none connected -na --clean max-order 2
(cd ~/devel/spel/src/ && make -j 8) && gdb --args spell-qtl -P auto -n test-2pop -wd /media/RAM/test-2pop -gm 100.map -p 100.popdata F2 100_F2.phen -p 100.popdata F2C 100_F2C.phen QTL-detection iQTLm cofactor-detection none connected -na max-order 2 --clean
2016-05-10 10:46:26.913543
POP A 1
POP F1 10
POP C 1
POP B 1
POP D 1
POP F1C 10
POP F2 10
POP F3 20
POP F2C 10
QTL 0.0 150.0
trait t1 qtl [('M_1_1', 0.0), ('M_1_2', 150.0)] effect [{'0': 1.0, '2': -1.0}, {'0': 1.0, '2': -1.0}] epistasis {} noise 1.0 0.0 2.0
trait t1 qtl [('M_1_1', 0.0), ('M_1_2', 150.0)] effect [{'0': 1.0, '2': 0.0}, {'0': 1.0, '2': 0.0}] epistasis {} noise 1.0 0.0 1.0
*ch1 2 M_1_1 150.0 M_1_2
generation;individual;mother;father
A;1;0;0
B;2;0;0
C;3;0;0
D;4;0;0
F1;5;1;2
F1;6;1;2
F1;7;1;2
F1;8;1;2
F1;9;1;2
F1;10;1;2
F1;11;1;2
F1;12;1;2
F1;13;1;2
F1;14;1;2
F1C;15;4;3
F1C;16;4;3
F1C;17;4;3
F1C;18;4;3
F1C;19;4;3
F1C;20;4;3
F1C;21;4;3
F1C;22;4;3
F1C;23;4;3
F1C;24;4;3
F2;25;7;7
F2;26;6;6
F2;27;14;14
F2;28;13;13
F2;29;11;11
F2;30;7;7
F2;31;7;7
F2;32;13;13
F2;33;14;14
F2;34;9;9
F2C;35;17;17
F2C;36;19;19
F2C;37;18;18
F2C;38;16;16
F2C;39;18;18