Evolutionary distance computation for BioSequence. #228

TransGirlCodes · 2016-07-26T09:56:09Z

Fulfills some of issue #266

This PR will start with Raw mutations counts, P distances, JC69, and K80. For BioSequences.

coveralls · 2016-07-26T10:13:12Z

Coverage increased (+0.02%) to 80.989% when pulling 7df3322 on evo_dist into cfaefd3 on master.

codecov-io · 2016-07-26T10:13:47Z

Current coverage is 82.20% (diff: 75.86%)

No coverage report found for master at 061e149.

Powered by Codecov. Last update 061e149...f9d0ecd

coveralls · 2016-07-26T13:49:19Z

Coverage decreased (-0.1%) to 80.822% when pulling fe986e4 on evo_dist into cfaefd3 on master.

coveralls · 2016-07-26T16:22:28Z

Coverage decreased (-0.1%) to 80.842% when pulling e8ceaac on evo_dist into e3b8ceb on master.

diegozea · 2016-07-26T16:56:23Z

src/phylo/distances.jl

+macro checkambig(expr)
+    quote
+        if isambiguous(a[i]) || isambiguous(b[i])
+            break


Why are you using break instead of throw an error?

It should be a continue not a break, that's a typo on my part.

coveralls · 2016-07-28T18:21:57Z

Coverage decreased (-0.2%) to 80.767% when pulling dde72d9 on evo_dist into e3b8ceb on master.

coveralls · 2016-07-29T23:35:28Z

Coverage decreased (-0.9%) to 80.763% when pulling 554b616 on evo_dist into 9cc8990 on master.

kdm9 · 2016-08-01T10:27:20Z

src/phylo/distances.jl

@@ -170,7 +232,58 @@ end

 # K80 Distance computation.

+<<<<<<< HEAD


Whoops! @Ward9250

I've seen it - it's gone on my uncommitted workings 😆. Code committed here might be messy in places for a while. I'm basing the design on a C design, which uses a lot of repetitive code, and macros. In julia, with generated functions, type hierarchy, and multiple dispatch I think we can do better and be more concise, but I'm still feeling my way to the best way of doing it.

Sounds awesome! Excuse the uninvited interjections, for some reason the diffs display in email alerts and though I'd let you know in case you missed it! Sorry for the noise.

This is not problematic for me at all, in fact we encourage such participation! :)

bicycle1885 · 2016-08-20T06:44:33Z

src/phylo/Phylo.jl

+    Kimura80,
+    distance,
+    Raw,        # alias for N_Mutations{DifferentMutation}
+    P,          # alias for P_Distance{DifferentMutation}


P and Raw looks too short and vague.

Ok it can be removed.

TransGirlCodes · 2016-08-20T10:42:26Z

@bicycle1885 Based on your comments I've changed N_Mutations{T} to Count{T}, and P_Distance{T} to Proportion{T}, removing the underscore, and I think, giving them both more semantic names e.g. I think the meaning of e.g. Count{Transitions} is clear, as is Proportion{Transitions}, indeed Proportion is more descriptive for people who have never heard of the measure referred to as a p-distance (Phylogeneticists and population geneticists certainly would have heard of p-distance, but other biologists may not have).

bicycle1885 · 2016-08-20T13:23:59Z

src/var/distances.jl

+# -----
+
+# Evolutionary distances
+abstract EvolutionaryDistances


Why is this plural?

bicycle1885 · 2016-08-20T13:35:00Z

src/var/distances.jl

+immutable Kimura80 <: TsTv end
+
+typealias JC69 JukesCantor69
+typealias K80 Kimura80


I think these type aliases are redundant. We should stick to use a single type name to avoid unnecessary confusion.

JC69 and K80 and other models in phylogenetics and evo.genetics have such few letter abbreviations that are commonly used, but they can be defined elsewhere in specific places if really needed, so I took them away.

coveralls · 2016-08-20T16:36:55Z

Coverage decreased (-0.03%) to 82.209% when pulling f9d0ecd on evo_dist into 10e6478 on master.

coveralls · 2016-08-20T16:36:55Z

Coverage decreased (-0.03%) to 82.209% when pulling f9d0ecd on evo_dist into 10e6478 on master.

TransGirlCodes · 2016-08-20T19:20:35Z

@bicycle1885 tests pass now 👍 if there's nothing else I'd like to merge and tick a few things off of #266.

bicycle1885 · 2016-08-20T19:29:07Z

src/var/Var.jl

+    JukesCantor69,
+    Kimura80,
+    JC69,       # alias for JukesCantor69
+    K80,        # alias for Kimura80


I guess these type aliases are already removed (a peculiar fact is that Julia doesn't warn you for this kind of mistakes).

That is indeed odd that the build didn't flag that up! :O

Ok just did a git commit amend, that should be gone now.

bicycle1885 · 2016-08-20T19:33:16Z

Okay, please go ahead .

coveralls · 2016-08-20T20:27:47Z

Coverage decreased (-0.03%) to 82.192% when pulling 3c1a893 on evo_dist into 061e149 on master.

coveralls · 2016-08-20T20:27:47Z

Coverage decreased (-0.03%) to 82.192% when pulling 3c1a893 on evo_dist into 061e149 on master.

TransGirlCodes added the stage: WIP label Jul 26, 2016

TransGirlCodes self-assigned this Jul 26, 2016

TransGirlCodes changed the title ~~Initial commit evo_dist~~ Computation of evolutionary distance between sequences. Jul 26, 2016

TransGirlCodes mentioned this pull request Jul 26, 2016

Evolutionary Distances JuliaStats/Distances.jl#53

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TransGirlCodes force-pushed the evo_dist branch from fe986e4 to e8ceaac Compare July 26, 2016 16:05

diegozea reviewed Jul 26, 2016
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TransGirlCodes force-pushed the evo_dist branch from dde72d9 to 554b616 Compare July 29, 2016 23:09

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TransGirlCodes force-pushed the evo_dist branch 9 times, most recently from 093cfcd to 3394d73 Compare August 2, 2016 15:06

TransGirlCodes force-pushed the evo_dist branch 2 times, most recently from 8fbdc36 to 2715c34 Compare August 17, 2016 12:46

TransGirlCodes changed the title ~~Computation of evolutionary distance between sequences.~~ Evolutionary distance computation for BioSequence. Aug 17, 2016

TransGirlCodes force-pushed the evo_dist branch 3 times, most recently from 9f2faf2 to dd6784c Compare August 17, 2016 23:11

bicycle1885 reviewed Aug 20, 2016
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Changes to distance type naming based on review comments.

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TransGirlCodes force-pushed the evo_dist branch from d76af82 to 8c4fbe8 Compare August 20, 2016 11:50

Bikeshedding: moved distance computation to Var module.

8c4fbe8

TransGirlCodes force-pushed the evo_dist branch from b385223 to cdeb1bc Compare August 20, 2016 13:22

Edited manual pages and docstrings for evolutionary distances

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bicycle1885 reviewed Aug 20, 2016
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src/var/distances.jl

# -----

# Evolutionary distances

abstract EvolutionaryDistances

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Why is this plural?

More rename

608ae2e

bicycle1885 reviewed Aug 20, 2016
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Ward9250 added 2 commits August 20, 2016 14:38

Typealiases gone

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Corrected tests

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TransGirlCodes force-pushed the evo_dist branch from f9d0ecd to 6d7980d Compare August 20, 2016 19:30

TransGirlCodes force-pushed the evo_dist branch from 6d7980d to 3c1a893 Compare August 20, 2016 20:00

Corrected line 132 of distances.jl

3c1a893

TransGirlCodes merged commit b798fd6 into master Aug 20, 2016

TransGirlCodes removed the stage: review label Aug 20, 2016

TransGirlCodes deleted the evo_dist branch August 20, 2016 20:26

richardreeve mentioned this pull request Sep 26, 2016

Phylogenetic diversity EcoJulia/Diversity.jl#5

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Evolutionary distance computation for BioSequence. #228

Evolutionary distance computation for BioSequence. #228

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coveralls commented Aug 20, 2016

		@@ -170,7 +232,58 @@ end

		# K80 Distance computation.

		<<<<<<< HEAD

Evolutionary distance computation for BioSequence. #228

Evolutionary distance computation for BioSequence. #228

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