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Operative system
Dear author,
Thanks for developing this very useful tool. Can it be used in Linux systems or is just for Windows? I work with Linux systems and it would be great to use it. Thank you.
Best,
Rom
Is it possible to use an available known ancestral genome to paint chromosomal rearrangement?
Thank you very much for this wonderful tool.
I wonder if we could use a known ancestral genome (instead of construct it) to analyze the genome rearrangement using this IAGS pipeline? For example, in my case, I am studying the Brassica genomes (including the 3 species that were included in Figure 3A of your paper (B. rapa, B. oleracea and B. nigra) and their ancestral genome tPCK. So, how one could just assign this tPCK genome as a common ancestral genome, and then analyze the rearrangement of the 22 genomic blocks in the extant genomes?
Thank you very much and I am looking forward to hearing from you.
Best regards,
Nam
question about chromosome painting
when I ran the painting.py I came across such a bug:
File "........./scenarios/inferringAncestorGenomeStructure/BlockMatchingOptimization.py", line 66, in <genexpr> (i[0][3] * match_matrix[int(i[0][1] / (self.__matching_dim1*2)), KeyError: (87, 1, 0)
It only appear when I draw the chromosome rearrangement plot for M.domestica (apple), it has undergone one WGD event. but for other species without WGD there is no problem. so it seems like the bug is related to WGD ?
How can I fix it. thank you !
reconstructed ancestral chromosomes with label "c"
Hi, in my analysis, some reconstructed ancestral chromosomes are labelled with "c", for example the last three ones:
s -4059 -4052 -4179 -4175 -4173 -4182 4169 -4164 -4161 -5030 -4203 -4198 -4188 -4127 -4123 -4115 -4112 -4110 -4131 -4141 -4136 -4065 4053 4050 4061 4057 4067 4089 4097 4099 -4910 -4911 4908 4875 -4844 4843 4840 4831 4865 4991 -4985 4846 4847 4849 -5231 -4839 -4836 -4834 -4833 -4832 -4830
s -4079 -4076 -4068 -4102 -4098 -4088 4138 4134 4140 4143 4145 4152 4155 4130 4111 4116 4119 4120 4126 4128 4144 4157 4159 4194 -4200 4205 4183 -4062 -4054 4063 4058 4105 -4146 -4148 -4150 -4154 4133 -4113 -5060 5082 -4117 -4121 -4129 -4158 -4186 -4204 4094
s 4236 -4235 4234 5176 4214 4215 -4216 -4222 4226 4227 4229 4230 4231 4232 -4247 4261 4262 4289 4291 -4293 5172 4296 4297 4299 4310 -4301 4303 -4304 4305 4306 4307 4308 4309 4266 4270 4970 4969 4966 4956 4954 4972 4951 5095 4957 -4763 -4764 -4766 4770 -4748 -4726 -5039 -5038 -5037
s -4253 -4576 -4578 -5023 -4518 -4516 -4461 4439 -4475 -4473 -4472 -4471 -4469 -4468 -4491 -5152 -4514 4510 -4509 -4505 -4504 -4502 -5154 -4500 -4496 -4494 -4428 -4425 -4375 -4365 -4369 -4381 -4386 4311 4594 4595 4607 4569 4537 4565 4551 4549 4279 4277 4275 -4271 4268 4267 -4264 4285 4286 -4302 4294 4290 -4082 -4087 -4095 -4093 -4055 -4162 4135 -4156 4125 -4166 -4180 5194 -4074 -4084 -4077 -4078 4075 4086 4104 4103 4321 5040 -4324 4333 4328 -4399 4872 -4871 -4870 4860 -4859 -4856 -4852 -4925 -4937 -4992 -4988 -4986
s -4327 -4334 4391 4396 4397 -4413 -4402 -4400 4405 4406 4409 4412 4377 5185 4380 -4382 4384 4312 4260 5177 4241 4242 4243 4244 4249 4973 4994 5002 5011 4975 4066 4096 -4091 4056 -4185 -4170 4192 4191 4190 4081 4083 4931 4933 -4149 -4317 -4919 -4884 -4893 -5226 -4620
s -4441 -4460 -4458 -4457 4456 -4455 -4454 -4464 -4451 -4450 -4446 -4445 -4444 -4443 -4588 -5133 -4583 4577 -4575 -4574 -4572 -4571 -4617
s 4528 -4527 -4526 -4525 -4524 -4523 -4521 -4519 -4540 -4542 -4563 -4562 -4561 -4560 -4557 -4556 4566 -4555 -4548 -4547 4416 -4593 -4415 4935 4934 4932 4947 -4955 -4857 -4678 4677 4695 4717 4716 4714 4702 4536 4554 4568 -4591 4580 -4541 4269 -4284 -4367 -4401 -4407 -4395 -4393 4326 -4344 -4913 -4676 -4823 -4773 -4734 -4762 4684 -4210 -4750 -4753 -4760 4959 4961 4971 4962 4963 4964 -4950 -4965 4949 -4948
s 4592 -4418 -4419 -4360 -4359 -4357 -4355 -4354 -4351 4340 4341 5049 -4887 -4885 -4898 -4899 4901 -4921 -4920 -5059 -4918 -4917 -4915 -4914 -4924 -4909 -4907 -4906 -4905 -4904 -4374 -4383 -4385 -4245 4246 -4248 -4259 -4251 -4258 -4233 -4224 -4288 -4292 4295 -4274 -4559 4902 4903 4371 4403 4394 4364 4325 4314 -5080 5062 4338 4882 4828 -4873 -4861 5114 4926 4987 4984
s -4616 -4614 -4613 -4612 -4611 -4610 -4609 -4605 -4604 -4603 4646 4668 4667 4661 4660 4654 4721 4722 4723 4796 4793 4792 4791 -4790 4789 4788 -4787 4786 5110 -4782 5108 4777 4800 4822 4821 4820 4819 4818 4815 4814 5071 4808 4807 -5136 -4767 -4768 -4725 4752 5160 4749 4806 4805 -5126 4741 5125 5211
s 4718 4715 -4713 -4712 -4720 -4707 4704 4280 4281 -5099 -4700 -4699 -4672 -4671 -4657 -4642 -4640 4558 4639 -4825 -4691 -4944 5001 -5004 -4993 -4990 -4826 4824 4942 4945 4946 4982 4981 4979 5028 5006 -5015 -5014 -5012 5008 -4943 4940 4939 5035 5021 -4929 4968 4953 4958 4674 4694 4709 4701 4641 4635 4632 4626 4666 -4653 4650 4649 4648 4795 4794 4775 4785 4811 4812 -4809 4738
c 4240 -4212
c -4422 -4424 -4435 -4498 -4499 -4501 4492 -4490 -4483 -4485 -4488 -4927 -4487 5149 -4484 -4482 -4481 4480 -4479 4476 -4420
c 4600 4601 -4645 -4644 -4643 -4597
Does this mean that they are circular? What do you think about this?
Thank you!
question about run Gramineae.py
when I run this Gramineae.py,
Error code 10009: License expired 2022-01-13
Traceback (most recent call last):
File "Gramineae.py", line 31, in
ancestor_name, dup_copy_number, out_copy_number, ancestor_target_copy_number)
File "/Users/luo/Desktop/IAGS/IAGS/models/MultiGGHPmodel.py", line 37, in MultiCopyGGHPmodel
adjacency_matrix = ggap.ancestor_adjacency_matrix()
File "/Users/luo/Desktop/IAGS/IAGS/inferringAncestorGenomeStructure/GGHP.py", line 224, in ancestor_adjacency_matrix
for v in self.__m.getVars():
AttributeError: 'GGHP' object has no attribute '_GGHP__m'
I have modified the corresponding file path, how to solve this error？ 🥹
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