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Example to discuss initial trees behavior #50

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f47f142
Add recomb to initial ts
ashander Nov 1, 2017
e44c298
Print trees and exit
ashander Nov 1, 2017
cda6666
Add seed (closes #51)
ashander Nov 1, 2017
4d7ecec
Test showing trees differ after one gen
ashander Nov 1, 2017
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12 changes: 9 additions & 3 deletions examples/examples.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@
help="name of file to output selected locus information", default="sel_loci.txt")
parser.add_argument("--treefile","-t", type=str, dest="treefile",
help="name of output file for trees (default: not output)",default=None)
parser.add_argument("--seed", "-d", dest="seed", type=int, help="random seed")

args = parser.parse_args()

Expand All @@ -56,6 +57,8 @@
import simuOpt
simuOpt.setOptions(alleleType='mutant')
import simuPOP as sim
sim.setRNG(seed=args.seed)
random.seed(args.seed)

def fileopt(fname,opts):
'''Return the file referred to by fname, open with options opts;
Expand Down Expand Up @@ -135,14 +138,17 @@ def __call__(self, loc, alleles):
id_tagger = sim.IdTagger()
id_tagger.apply(pop)
first_gen = pop.indInfo("ind_id")
init_ts = msprime.simulate(2*len(first_gen),
length=max(locus_position))
length = max(locus_position)

# Since we want to have a finite site model, we force the recombination map
# to have exactly `length` loci with a fixed recombination rate between them.
rcmb_map = msprime.RecombinationMap.uniform_map(length, args.recomb_rate, length)
init_ts = msprime.simulate(2*len(first_gen), recombination_map=rcmb_map)
haploid_labels = [(k,p) for k in first_gen
for p in (0,1)]
node_ids = {x:j for x, j in zip(haploid_labels, init_ts.samples())}
rc = RecombCollector(ts=init_ts, node_ids=node_ids,
locus_position=locus_position)

# initially, population is monogenic
init_geno=[sim.InitGenotype(freq=1.0)]

Expand Down
8 changes: 8 additions & 0 deletions examples/proc.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
# coding: utf-8
import msprime
ts = msprime.load('neutral_ts')
tsc = msprime.TreeStatCalculator(ts)
print('mean pairwise tmrca matrix among all 6 haploid samples for 10 windows on genome')
for t in tsc.mean_pairwise_tmrca(windows=[float(i) for i in range(10)],
sample_sets=[[0,1,2,3,4,5], [0,1,2,3,4,5]]):
print(t)
6 changes: 6 additions & 0 deletions examples/test.sh
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@@ -0,0 +1,6 @@
echo "trees differ across genome with recombination"
python ./examples.py -d 111 -T 1 -N 3 -r 1e-1 -L 10 -a 0.0001 -b 0.0001 -k 3 -t neutral_ts -g /dev/null > /dev/null && python proc.py
echo " "
echo "trees conserved across genome without recombination"
python ./examples.py -d 111 -T 1 -N 3 -r 0 -L 10 -a 0.0001 -b 0.0001 -k 3 -t neutral_ts -g /dev/null > /dev/null && python proc.py

132 changes: 132 additions & 0 deletions examples/tree_comparison.txt
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@@ -0,0 +1,132 @@
simuPOP Version 1.1.8.3 : Copyright (c) 2004-2016 Bo Peng
Revision 4553 (Feb 11 2017) for Python 3.5.3 (64bit, 1thread)
Random Number Generator is set to mt19937 with random seed 0x62d96efe2e082f18.
This is the standard mutant allele version with 256 maximum allelic states.
For more information, please visit http://simupop.sourceforge.net,
or email [email protected] (subscription required).
Options:
Namespace(chrom_length=10, gamma_alpha=0.0001, gamma_beta=0.0001, generations=10000, logfile='-', neut_mut_rate=1e-07, nsamples=5000, nselloci=1, outfile=None, popsize=2, recomb_rate=0.1, sel_mut_rate=1e-07, selloci_file='sel_loci.txt', simplify_interval=500, treefile='neutral_ts')
10:09:07 11/01/17 PDT
----------

Init ts
############################################################
# Nodes #
############################################################
id flags population time
0 1 0 0.00000000000000
1 1 0 0.00000000000000
2 1 0 0.00000000000000
3 1 0 0.00000000000000
4 0 0 0.24138545192840
5 0 0 0.36768962082101
6 0 0 0.80818994340547
7 0 0 1.10295116208317
8 0 0 1.21146637134289
9 0 0 1.55374021332996
10 0 0 1.90995962338469
11 0 0 3.09020402491767
12 0 0 4.12376873296128
############################################################
# Edges #
############################################################
id left right parent child
0 0.00000000 9.00000000 4 2
1 0.00000000 9.00000000 4 3
2 2.00000000 3.00000000 5 1
3 2.00000000 3.00000000 5 4
4 0.00000000 2.00000000 6 0
5 0.00000000 2.00000000 6 4
6 2.00000000 4.00000000 7 0
7 3.00000000 4.00000000 7 4
8 2.00000000 3.00000000 7 5
9 8.00000000 9.00000000 8 0
10 0.00000000 2.00000000 8 1
11 8.00000000 9.00000000 8 4
12 0.00000000 2.00000000 8 6
13 7.00000000 8.00000000 9 1
14 7.00000000 8.00000000 9 4
15 4.00000000 7.00000000 10 1
16 4.00000000 7.00000000 10 4
17 4.00000000 5.00000000 11 0
18 3.00000000 4.00000000 11 1
19 3.00000000 4.00000000 11 7
20 4.00000000 5.00000000 11 10
21 5.00000000 8.00000000 12 0
22 8.00000000 9.00000000 12 1
23 8.00000000 9.00000000 12 8
24 7.00000000 8.00000000 12 9
25 5.00000000 7.00000000 12 10
############################################################
# Sites #
############################################################
id position ancestral_state
############################################################
# Mutations #
############################################################
id site node derived_state parent
############################################################
# Migrations #
############################################################
id left right node source dest time

In recomb collector
############################################################
# Nodes #
############################################################
id flags population time
0 1 0 0.00000000000000
1 1 0 0.00000000000000
2 1 0 0.00000000000000
3 1 0 0.00000000000000
4 0 0 0.24138545192840
5 0 0 0.36768962082101
6 0 0 0.80818994340547
7 0 0 1.10295116208317
8 0 0 1.21146637134289
9 0 0 1.55374021332996
10 0 0 1.90995962338469
11 0 0 3.09020402491767
12 0 0 4.12376873296128
############################################################
# Edges #
############################################################
id left right parent child
0 0.00000000 9.00000000 4 2
1 0.00000000 9.00000000 4 3
2 2.00000000 3.00000000 5 1
3 2.00000000 3.00000000 5 4
4 0.00000000 2.00000000 6 0
5 0.00000000 2.00000000 6 4
6 2.00000000 4.00000000 7 0
7 3.00000000 4.00000000 7 4
8 2.00000000 3.00000000 7 5
9 8.00000000 9.00000000 8 0
10 0.00000000 2.00000000 8 1
11 8.00000000 9.00000000 8 4
12 0.00000000 2.00000000 8 6
13 7.00000000 8.00000000 9 1
14 7.00000000 8.00000000 9 4
15 4.00000000 7.00000000 10 1
16 4.00000000 7.00000000 10 4
17 4.00000000 5.00000000 11 0
18 3.00000000 4.00000000 11 1
19 3.00000000 4.00000000 11 7
20 4.00000000 5.00000000 11 10
21 5.00000000 8.00000000 12 0
22 8.00000000 9.00000000 12 1
23 8.00000000 9.00000000 12 8
24 7.00000000 8.00000000 12 9
25 5.00000000 7.00000000 12 10
############################################################
# Sites #
############################################################
id position ancestral_state
############################################################
# Mutations #
############################################################
id site node derived_state parent
############################################################
# Migrations #
############################################################
id left right node source dest time