dereneaton / simrrls Goto Github PK

Hi

I installed simrrls using egglib 3.0.0b5 as well as egglib 3.0.0b6. (tested and working according to the egglib homepage)
Running simrrls -h works but running the example usages always results in errors:

$ simrrls -o test1 -N 1e6 -n 4 -L 1000
Traceback (most recent call last):
File "/usr/local/anaconda/envs/simrrls_egglib_old/bin/simrrls", line 9, in
load_entry_point('simrrls==0.0.10', 'console_scripts', 'simrrls')()
File "/usr/local/anaconda/envs/simrrls_egglib_old/lib/python2.7/site-packages/simrrls/main.py", line 17, in main
run(params)
File "/usr/local/anaconda/envs/simrrls_egglib_old/lib/python2.7/site-packages/simrrls/simrrls.py", line 464, in run
tiptax, paramset = checkopts(params)
File "/usr/local/anaconda/envs/simrrls_egglib_old/lib/python2.7/site-packages/simrrls/simrrls.py", line 29, in checkopts
tiptax, paramset = defaulttree(params)
File "/usr/local/anaconda/envs/simrrls_egglib_old/lib/python2.7/site-packages/simrrls/simrrls.py", line 87, in defaulttree
paramset = egglib.simul.CoalesceParamSet(
AttributeError: 'module' object has no attribute 'simul'

Is this an actual error in the code or am I missing some files? I followed the installation steps outlined on the github page... the simrrls is installed an anaconda test environment.

Additional infos/versions:

$ python --version
Python 2.7.11 :: Continuum Analytics, Inc.

$ simrrls --version
simrrls 0.0.10

import egglib
print egglib.version
3.0.0b6

Does anybody else have this problem? Thanks for any hints....

I get this error when I try to use an INDEL rate > 0.1:

simrrls -I 0.02

Traceback (most recent call last):
  File "/usr/bin/simrrls", line 9, in <module>
    load_entry_point('simrrls==0.0.9', 'console_scripts', 'simrrls')()
  File "/usr/lib/python2.7/site-packages/simrrls/__main__.py", line 17, in main
    run(params)
  File "/usr/lib/python2.7/site-packages/simrrls/simrrls.py", line 538, in run
    counter, stepsize)
  File "/usr/lib/python2.7/site-packages/simrrls/simrrls.py", line 358, in seq_copies
    if tempseq[iloc] != outseq[iloc]:
IndexError: string index out of range

Hi Deren,

I was trying to provide user defined input tree but it does not work (got stuck there without any error messages). Could you please try and see whether you can reproduce the problem? Thanks!

The tree I used is a random 30 species ultrametric one (sp30.tre):
((((t3:0.03546664747,t10:0.03546664747):0.03542769548,((((t20:0.01022248237,t14:0.01022248237):0.006643977943,(t17:0.01408948611,t8:0.014089
48611):0.002776974204):0.01860290103,t16:0.03546936135):0.02307928936,(((t5:0.01379999717,t25:0.01379999717):0.01338132237,t24:0.02718131954
):0.01981542818,(t19:0.01829421996,t18:0.01829421996):0.02870252776):0.01155190299):0.01234569224):0.009261864559,(t1:0.04826562616,(t13:0.0
2627695183,t15:0.02627695183):0.02198867433):0.03189058135):0.01984379249,(((t28:0.04598097632,((t22:0.01661648246,t11:0.01661648246):0.0250
1832827,((t21:0.0196005595,(t26:0.008929907245,t7:0.008929907245):0.01067065225):0.007131581783,((t4:0.006193304346,t9:0.006193304346):0.010
45860409,t2:0.01665190844):0.01008023284):0.01490266944):0.004346165601):0.006363314203,t23:0.05234429053):0.01214267362,((t12:0.03181285344
,((t27:0.01327667385,t6:0.01327667385):0.003038107994,t29:0.01631478184):0.0154980716):0.01010201049,t30:0.04191486393):0.02257210022):0.035
51303585);

The command I used is:
simrrls -o test -L 1 -t sp30.tre -dm 1 -ds 0

Cheers,
Huan

Hi,
I have run into a similar problem as reported in issue #3.

When I call simrrls I get the following error message:
$ simrrls
Traceback (most recent call last):
File "/Users/ClaudiaPaetzold/anaconda2/bin/simrrls", line 9, in
load_entry_point('simrrls==0.0.10', 'console_scripts', 'simrrls')()
File "build/bdist.macosx-10.5-x86_64/egg/simrrls/main.py", line 17, in main
File "build/bdist.macosx-10.5-x86_64/egg/simrrls/simrrls.py", line 464, in run
File "build/bdist.macosx-10.5-x86_64/egg/simrrls/simrrls.py", line 29, in checkopts
File "build/bdist.macosx-10.5-x86_64/egg/simrrls/simrrls.py", line 87, in defaulttree
AttributeError: 'module' object has no attribute 'simul'

However, following your advice from issue #3 I have installed eggless v2.1.11.
Yet the error remains.
Any hints?

P.S. python v 2.7.11
numpy v1.11.0

Any help is appreciated. Thank You

Hi,
First, thank you for writing this package, a simulator serves a lot of purposes !
I'm trying to simulate paired end ddRAD data for practice testing different pipelines and I have a couple of questions. What type of input does simrrls use ? and what is the option for the input ?
Does the tool simulate SNPs? if yes, how would u know where they are?

Regards
Shruti

Using the -c1 or -c2 option has no effect on output.