#!/usr/bin/env python
# coding: utf-8

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import ipyrad as ip


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data = ip.Assembly("test")


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data.set_params("project_dir", "sixseven")
data.set_params("raw_fastq_path", "./ipsimdata/rad_example_R1_.fastq.gz")
data.set_params("barcodes_path", "./ipsimdata/rad_example_barcodes.txt")


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data.run("12345")


# ### Set populations

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# define the groups
popdata = {
    "1": [i for i in data.samples if "1" in i], 
    "2": [i for i in data.samples if "2" in i],
    "3": [i for i in data.samples if "3" in i],
    }

# mincov values for the groups
popmins = {"1": 3, "2": 3, "3": 3}

# link the two dictionaries into a populations attribute
data._link_populations(popdict=popdata, popmins=popmins)

# view populations
data.populations


# ### run six and seven with pops

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data.run("6")


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data.run("7")


# ### But, now if we branch it breaks

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# branch assembly
d2 = data.branch("d2", subsamples=[i for i in data.samples if i != "1A_0"])

# update pops to match new samples 
d2.populations['1'] = (3, ['1B_0', '1C_0', '1D_0'])

# run 7
d2.run("7", force=True)


# ### The same above retried after fix to code

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import ipyrad as ip


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d2 = ip.load_json("sixseven/d2.json")
d2.run("7", force=True)


# ### modify pops again

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# update pops to be diff from samples
d2.populations['1'] = (2, ['1C_0', '1D_0'])

# run 7
d2.run("7", force=True)


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# update pops to be diff from samples
d3 = d2.branch("d3", subsamples=[i for i in d2.samples if i != "1B_0"])
d3.populations['1'] = (2, ['1C_0', '1D_0'])

# run 7
d3.run("7", force=True)


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