Metaphlan and Humann tutorials #63

kescobo · 2021-10-05T02:24:34Z

No description provided.

annelle-abatoni · 2021-10-06T15:11:47Z

I am wondering why conda.md was deleted? Is it not needed to run functions anymore?

annelle-abatoni · 2021-10-06T15:14:42Z

I am wondering why conda.md was deleted? Is it not needed to run functions anymore?

Oh, I can see that it's mentioned in docs/src/gettingstarted.md which I think answers my question...

annelle-abatoni · 2021-10-06T21:45:10Z

It seems that tutorial.md contains metaphlan functions, and I was wondering if we're going to be keeping it like that or shifting them to metaphlan.md?

docs/src/humann.md

annelle-abatoni · 2021-10-06T22:16:00Z

I am not sure what the rules on this are, but do you think it would be helpful to add a link to every method mentioned that points to its respective functionality in a src file. Like CommunityProfile instead of CommunityProfile

I think this would be even more helpful when pointing to files.

anikaluo · 2021-10-06T22:39:04Z

Not sure why but I get this error when I try to run metaphlan (Line 91):

julia> metaphlan("SRS014476-Supragingival_plaque.fasta.gz", "SRS014476-Supragingival_plaque_profile.tsv"; input_type="fasta")
[ Info: Running command: `metaphlan SRS014476-Supragingival_plaque.fasta.gz SRS014476-Supragingival_plaque_profile.tsv --input_type fasta`
ERROR: IOError: could not spawn `metaphlan SRS014476-Supragingival_plaque.fasta.gz SRS014476-Supragingival_plaque_profile.tsv --input_type fasta`: no such file or directory (ENOENT)

anikaluo · 2021-10-06T22:41:24Z

It seems that tutorial.md contains metaphlan functions, and I was wondering if we're going to be keeping it like that or shifting them to metaphlan.md?

Yes, I wrote that tutorial and named it as such because I thought the tutorials were all going to be in one file. We can absolutely delete it if there's no new info in it.

annelle-abatoni · 2021-10-06T23:18:31Z

It seems that tutorial.md contains metaphlan functions, and I was wondering if we're going to be keeping it like that or shifting them to metaphlan.md?

Yes, I wrote that tutorial and named it as such because I thought the tutorials were all going to be in one file. We can absolutely delete it if there's no new info in it.

Oh I see. I think because right now tutorial.md has all the functions and examples of metaphlan.jl and that what's missing in metaphlan.md, we can just shift those to metaphlan.md and be done with that tutorial, and then delete the tutorial.md file.

kescobo · 2021-10-08T01:31:46Z

Alright, finally back to at least some tests passing. I'm gonna merge this now. @anikaluo @annelle-abatoni can you checkout main and run tests on your mac to see if they pass for you? You should make sure to ]add Microbiome#main or ]dev Microbiome if you haven't already

anikaluo · 2021-10-08T02:04:45Z

all tests pass locally for me!
should we now branch and comment on main? how should we review the tutorials now?

kescobo · 2021-10-08T02:06:53Z

yay!

The humann tutorial should be good to review now. Metaphlan needs work

anikaluo · 2021-10-08T02:08:49Z

oh can we still review this PR even after it's merged?

kescobo · 2021-10-08T02:39:48Z

Yep! But you can also make a review PR

docs/src/humann.md

docs/src/gettingstarted.md

docs/src/humann.md

docs/src/gettingstarted.md

docs/src/humann.md

anikaluo · 2021-10-11T20:57:29Z

docs/src/humann.md

+If you just want a single value, you can use a `GeneFunction` directly:
+
+```julia-repl
+julia> gfs_strat[GeneFunction("UniRef90_D0TRR5", "Bacteroides_dorei"), 1]


Should this actually be something like this:

julia> gfs_strat[GeneFunction("UniRef90_D0TRR5", Taxon("Bacteroides_dorei", :species)), 1] 0.8271298594

When I run the line as is, I get a huge error that starts with ERROR: BoundsError: attempt to access Axis(GeneFunction[GeneFunction("UNMAPPED", missing), ...

anikaluo · 2021-10-11T21:09:42Z

docs/src/humann.md

+
+In the following example, `gf ->` indicates a function that takes a single argument
+(in this case, our `GeneFunction`),
+then askes if it's [`name`](@ref) is "UNMAPPED" with `name(gf) == "UNMAPPED"`,


"askes" --> "asks" typo

broken link for name?

anikaluo · 2021-10-11T21:11:38Z

docs/src/humann.md

+
+Note - to get other feature types, you may have to download the requisite databases
+using `humann_databases` at the command line.
+See [Using Conda.jl](@ref)


broken link
I think it should be [Using Conda.jl](@ref using-conda)?

(because Getting Started line 136: ### [Using Conda.jl](@id using-conda))

anikaluo · 2021-10-11T21:29:58Z

docs/src/humann.md

+Process(`humann_join_tables -i hmp_subset -o hmp_subset_genefamilies.tsv --file_name genefamilies`, ProcessExited(0))
+```
+
+This will write a new file that you can then load with [`humann_profiles`](@ref)


Should humann_profiles have a docstring?

anikaluo · 2021-10-11T21:30:39Z

docs/src/humann.md

+This will write a new file that you can then load with [`humann_profiles`](@ref)
+
+```julia-repl
+julia> humann_profiles("hmp_subset_genefamilies.tsv"; stratified=true)


add output?

julia> humann_profiles("hmp_subset_genefamilies.tsv"; stratified=true) CommunityProfile{Float64, GeneFunction, MicrobiomeSample} with 1 features in 6 samples Feature names: UNMAPPED Sample names: SRS014459-Stool_Abundance-RPKs, SRS014464-Anterior_nares_Abundance-RPKs, SRS014470-Tongue_dorsum_Abundance-RPKs...SRS014476-Supragingival_plaque_Abundance-RPKs, SRS014494-Posterior_fornix_Abundance-RPKs

I guess it's the same output as below, but it could be helpful to have it here too

anikaluo · 2021-10-11T21:40:44Z

docs/src/humann.md

+                      sort="braycurtis",
+                      scaling="logstack",
+                      as_genera=true,
+                      remove_zeros=true)


Should humann_barplot calls all have full outputs (1 and 2 have partial, 3 and 4 have full, 5 does not have an output at all)

Here's my outputs:

julia> humann_barplot(gfs, "plot1.png"; focal_metadata="STSite", focal_feature="METSYN-PWY") Process(`humann_barplot --i /var/folders/n6/jnm06kv91t7gl5jy43j3smcr0000gn/T/jl_QMapSq -o plot1.png --last-metadata STSite --focal-metadata STSite --focal-feature METSYN-PWY`, ProcessExited(0)) julia> humann_barplot(gfs, "plot2.png"; focal_metadata="STSite", focal_feature="METSYN-PWY", sort="sum") Process(`humann_barplot --i /var/folders/n6/jnm06kv91t7gl5jy43j3smcr0000gn/T/jl_cLL6XK -o plot2.png --last-metadata STSite --focal-metadata STSite --focal-feature METSYN-PWY --sort sum`, ProcessExited(0)) julia> humann_barplot(gfs, "plot3.png"; focal_metadata="STSite", focal_feature="METSYN-PWY", sort=["sum", "metadata"], scaling="logstack") Process(`humann_barplot --i /var/folders/n6/jnm06kv91t7gl5jy43j3smcr0000gn/T/jl_dQCVFF -o plot3.png --last-metadata STSite --focal-metadata STSite --focal-feature METSYN-PWY --sort sum metadata --scaling logstack`, ProcessExited(0)) julia> humann_barplot(gfs, "plot4.png"; focal_metadata="STSite", focal_feature="COA-PWY", sort="sum") Process(`humann_barplot --i /var/folders/n6/jnm06kv91t7gl5jy43j3smcr0000gn/T/jl_nXUvHy -o plot4.png --last-metadata STSite --focal-metadata STSite --focal-feature COA-PWY --sort sum`, ProcessExited(0)) julia> humann_barplot(gfs, "plot5.png"; focal_metadata="STSite", focal_feature="COA-PWY", sort="braycurtis", scaling="logstack", as_genera=true, remove_zeros=true) Process(`humann_barplot --i /var/folders/n6/jnm06kv91t7gl5jy43j3smcr0000gn/T/jl_qYK7Ou -o plot5.png --last-metadata STSite --focal-metadata STSite --focal-feature COA-PWY --sort braycurtis --scaling logstack --as-genera --remove-zeros`, ProcessExited(0))

kescobo · 2021-10-12T14:35:14Z

Pretty sure a bunch of these things have been fixed in recent PRs. Let's put a pause on reviewing here and make sure everyone is on the most up-to-date version tomorrow

add skeleton tutorials

c42f97c

kescobo added Complexity: medium docs labels Oct 5, 2021

kescobo added 7 commits October 4, 2021 22:33

fix links

1880302

add more to getting started

5f87dbe

finish getting started

5394095

add metaphlan function

316ea2d

add first step on metaphlan tutorial

f0cf57d

add info on installing humann databases

b138431

first step of humann tutorial

df7291e

kescobo added 10 commits October 6, 2021 13:59

add slicing to humann tutorial

1c554a6

some anika fixes

fc62748

some anika fixes

983c301

make CSV.write work for gene functions

80faa79

working CSV roundtrip for humann profiles

662780c

revive humann_regroup and humann_rename

eb5660b

add humann_renorm

083b68c

update docstrings

ded46d0

don't inlcude documenter manifest

c8fd078

add bits on other humann utilities

b6bd957

annelle-abatoni reviewed Oct 6, 2021

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make read_pcl

fbe3e28

kescobo force-pushed the tutorials branch from a8d41b8 to fbe3e28 Compare October 7, 2021 13:32

kescobo merged commit e789299 into main Oct 8, 2021

kescobo deleted the tutorials branch October 8, 2021 01:31

kescobo mentioned this pull request Oct 8, 2021

Deprecate permanova in favor of hydra #55

Closed

This was referenced Oct 8, 2021

Make sure all DataFrames - returning functions switch to comm profile #30

Closed

Plotting #25

Open

Metadata import into microbial communities #24

Closed

I/O For other biobakery outputs #23

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Metaphlan and Humann tutorials #63

Metaphlan and Humann tutorials #63

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kescobo commented Oct 12, 2021

Metaphlan and Humann tutorials #63

Metaphlan and Humann tutorials #63

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