I'm getting different results when I run yardoc vs when I run rake yard
$ yardoc
Files: 123
Modules: 4 ( 0 undocumented)
Classes: 120 ( 0 undocumented)
Constants: 11 ( 0 undocumented)
Attributes: 16 ( 0 undocumented)
Methods: 440 ( 0 undocumented)
100.00% documented
$ rake yard
Files: 123
Modules: 4 ( 0 undocumented)
Classes: 120 ( 0 undocumented)
Constants: 11 ( 0 undocumented)
Attributes: 16 ( 0 undocumented)
Methods: 544 ( 2 undocumented)
99.71% documented
I'm not sure where the extra 104 methods are coming from, or which 2 of them aren't documented yet. Is it coming from my gems?
I've tried looking for an answer but haven't found anything. Can somebody point me in the right direction to explain this discrepancy, or whether it really matters?
I've also tried running $ yard --list-nodoc but it gives me similar results to $ yardoc; which is why I'm asking.
The YARD README should have the info you need. In particular, the yarddoc command "will assume your files are located in the lib/ directory", but this behavior can be customized in a .yardopts file.
Similarly, rake yard by default looks for files matching lib/**/*.rb, but this can be customized in the Rakefile, e.g.:
require 'yard'
YARD::Rake::YardocTask.new do |t|
t.files = ['lib/**/*.rb', OTHER_PATHS]
end
TL;DR: check the project's .yardopts and Rakefile files.
Related
Pylint exited with code 28 on Linux run. What does this error code mean?
I know it doesn't mean low on space as I tried the same command on a empty VM.
Answer + Examples:
(Note the pylint exit codes table below from pylint official site.
pylint exit codes conforms to 2 to the power of x (x = 0 to 5)
This is a crystal clear sign that they use a binary system for exit codes, this means that (as mentioned in the example within the image below) if exit code is:
28 - in binary: 0001 1100 (exit code 4, 8, 16 was triggered at least once for each)
63 - in binary: 0011 1111 (all error codes was triggered at least once for each which is the maximum errors combined)
Pyline exit code 28 on Linux and exit code 30 on Windows both mean that the config file that you are feeding in has an invalid configuration.
For me that was having underscores separating words instead of dashes. I had changed this because the wheel build deprecated dashes for flake8 and mypy but pylint needs to remain with dashes separating the words.
I want to list all processes running on my Windows system using Ruby without installing any additional dependency or library that is not already part of Ruby. I have not found any way to do this online. Is there any clean way to do this from Ruby?
You can use the Kernal::system method to execute a command line argument. For example:
system("tasklist")
Image Name PID Session Name Session# Mem Usage
========================= ======== ================ =========== ============
System Idle Process 0 Services 0 24 K
...
ruby.exe 1336 Console 1 9,100 K
tasklist.exe 944 Console 1 5,332 K
Alternately--as points #Pavling out--you can use [Kernal::`](aka backtick), but some find it less readable. YMMV.
Need to recruit the help of any budding bioinformaticians that are lurking in the shadows here.
I am currently in the process of formatting some .fasta files for use in a set of grouping programs but I cannot for the life of me get them to work. First things first, all the files have to have a 3 or 4 character name such as the following:
PP41.fasta
PP59.fasta
PPBD.fasta
...etc...
The files must have headers for each gene sequence that look like so: >xxxx|yyyyyyyyyy where xxxx is the same 3 or 4 letter 'taxon' identifier as the file names I put above and yyyyyyy is a numerical identifier for each of the proteins within each of the taxons (the pipe symbol can also be replaced with an _ as below). I then cat all of these in to one file which has a header that looks correct like so:
>PP49_00001
MIENFNENNDMSDMFWEVEKGTGEVINLVPNTSNTVQPVVLMRLGLFVPTLKSTKRGHQG
EMSSMDATAELRQLAIVKTEGYENIHITGARLDMDNDFKTWVGIIHSFAKHKVIGDAVTL
SFVDFIKLCGIPSSRSSKRLRERLGASLRRIATNTLSFSSQNKSYHTHLVQSAYYDMVKD
TVTIQADPKIFELYQFDRKVLLQLRAINELGRKESAQALYTYIESLPPSPAPISLARLRA
RLNLRSRVTTQNAIVRKAMEQLKGIGYLDYTEIKRGSSVYFIVHARRPKLKALKSSKSSF
KRKKETQEESILTELTREELELLEIIRAEKIIKVTRNHRRKKQTLLTFAEDESQ*
>PP49_00002
MQNDIILPINKLHGLKLLNSLELSDIELGELLSLEGDIKQVSTGNNGIVVHRIDMSEIGS
FLIIDSGESRFVIKAS*
Next step is to construct a blast database which I do as follows, using the formatdb tool of NCBI Blast:
formatdb -i allproteins.fasta -p T -o T
This produces a set of files for the database. Next I conduct an all-vs-all BLAST of the concatenated proteins against the database that I made of them like so, which outputs a tabular file which I suspect is where my issues are beginning to arise:
blastall -p blastp -d allproteins.fasta -i allproteins.fasta -a 6 -F '0 S' -v 100000 -b 100000 -e 1e-5 -m 8 -o plasmid_allvall_blastout
These files have 12 columns and look like the below. It appears correct to me, but my supervisor suspects the error is in the blast file - I don't know what I'm doing wrong however.
PP49_00001 PP51_00025 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PP49_00001 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PPTI_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPNP_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPKC_00016 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPBD_00021 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPJN_00003 91.14 79 7 0 145 223 2 80 8e-47 147
PP49_00002 PPTI_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPNP_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPKC_00018 100.00 76 0 0 1 76 1 76 3e-50 146
SO, this is where the problems really begin. I now pass the above file to a program called orthAgogue which analyses the paired sequences I have above using parameters laid out in the manual (still no idea if I'm doing anything wrong) - all I know is the several output files that are produced are all just nonsense/empty.
Command looks like so:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O .
Any and all ideas welcome! (Hope I've covered everything - sorry about the long post!)
EDIT Never did manage to find a solution to this. Had to use an alternative piece of software. If admins wish to close this please do, unless it is worth having open for someone else (though I suspect its a pretty niche issue).
Discovered this issue (of orthAgogue) first today:
though my reply may be old, I hope it may help future users;
issue is due to a missing parameter: seems like you forgot to specify the separator: -s '_', ie, the following set of command-line parameters should do the trick*:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O -s '_'
(* Under the assumption that your input-file is a tabular-seperated file of columns.)
A brief update after comment made by Joe:
In brief, the problem described in the intiail error report (by Joe) is (in most cases) not a bug. Instead it is one of the core properties of the Inparanoid algorithm which orthAgogue implements: if your ortholog-result-file is empty (though constructed), this (in most cases) implies that there are no reciprocal best match between a protein-pair from two different taxa/species.
One (of many) explanations for this could be that your blastp-scores are too similar, a case where I would suggest a combined tree-based/homology clustering as in TREEFAM.
Therefore, when I receive your data, I'll send it to one of the biologists I'm working with, with goal of identifying the tool proper for your data: hope my last comment makes your day ;)
Ole Kristian Ekseth, developer of orthAgogue
In an effort to use Cucumber for a command-line script, I've installed the aruba gem as per the instructions provided. It's in my Gemfile, I can verify that the correct version is installed and I've included
require 'aruba/cucumber'
in 'features/env.rb'
In order to ensure it works, I wrote the following scenario:
#announce
Scenario: Testing cucumber/aruba
Given a blank slate
Then the output from "ls -la" should contain "drw"
assuming the thing should fail.
It does fail, but it fails for the wrong reasons:
#announce
Scenario: Testing cucumber/aruba
Given a blank slate
Then the output from "ls -la" should contain "drw"
You have a nil object when you didn't expect it!
You might have expected an instance of Array.
The error occurred while evaluating nil.[] (NoMethodError)
features/dataloader.feature:9:in `Then the output from "ls -la" should contain "drw"'
Anyone have any ideas why this isn't working? This seems to be very basic aruba behavior.
You are missing a 'When' step - the aruba "output should contain" step requires the command to have already run (it does not run it itself, it only looks it up).
#announce
Scenario: Testing cucumber/aruba
Given a blank slate
When I run `ls -la`
Then the output from "ls -la" should contain "drw"
This produces, on my machine:
#announce
Scenario: Testing cucumber/aruba # features/test_aruba.feature:8
When I run `ls -la` # aruba-0.4.11/lib/aruba/cucumber.rb:56
$ cd /Users/d.chetlin/dev/mine/ladder/tmp/aruba
$ ls -la
total 0
drwx------ 2 d.chetlin staff 68 Feb 15 23:38 .
drwx------ 7 d.chetlin staff 238 Feb 15 23:38 ..
Then the output from "ls -la" should contain "drw" # aruba-0.4.11/lib/aruba/cucumber.rb:86
1 scenario (1 passed)
2 steps (2 passed)
0m0.465s
I have a pretty big spec suite (watirspec), I am running it against a Ruby gem (safariwatir) and there are a lot of failures:
1002 examples, 655 failures, 1 pending
When I make a change in the gem and run the suite again, sometimes a lot of previously failing specs pass (52 in this example):
1002 examples, 603 failures, 1 pending
I would like to know which previously failing specs are now passing, and of course if any of the previously passing specs are now failing. What I do now to compare the results is to run the tests with --format documentation option and output the results to a text file, and then diff the files:
rspec --format documentation --out output.txt
Is there a better way? Comparing text files is not the easiest way to see what changed.
Just save the results to file like you're doing right now and then just diff those results with some random diff-ing tool.
I don't know of anything out there that can do exactly that. Said that, if you need it so badly you don't mind spending some time hacking your own formatter, take a look at Spec::Runner::Formatter::BaseFormatter.It is pretty well documented.
I've implemented #Serabe's solution for you. See the gist: https://gist.github.com/1142145.
Put the file my_formatter.rb into your spec folder and run rspec --formatter MyFormatter. The formatter will compare current run result with previous run result and will output the difference as a table.
NOTE: The formatter creates/overwrites file result.txt in the current folder.
Example usage:
D:\Projects\ZPersonal\equatable>rspec spec --format MyFormatter
..........
No changes since last run
Finished in 0.011 seconds
10 examples, 0 failures
No changes since last run line was added by the formatter.
And now I intentionally broken one and rerun rspec:
D:\Projects\ZPersonal\equatable>rspec spec --format MyFormatter
..F.......
Affected tests (1).
PS CS Description
. F Equatable#== should be equal to the similar sock
PS - Previous Status
CS - Current Status
Failures:
1) Equatable#== should be equal to the similar sock
Failure/Error: subject.should == Sock.new(10, :black, 0)
expected: #<Sock:0x2fbb930 #size=10, #color=:black, #price=0>
got: #<Sock:0x2fbbae0 #size=10, #color=:black, #price=20> (using ==)
Diff:
## -1,2 +1,2 ##
-#<Sock:0x2fbb930 #color=:black, #price=0, #size=10>
+#<Sock:0x2fbbae0 #color=:black, #price=20, #size=10>
# ./spec/equatable_spec.rb:30:in `block (3 levels) in <top (required)>'
Finished in 0.008 seconds
10 examples, 1 failure
Failed examples:
rspec ./spec/equatable_spec.rb:29 # Equatable#== should be equal to the similar sock
The table with affected specs was added by the formatter:
Affected tests (1).
PS CS Description
. F Equatable#== should be equal to the similar sock
PS - Previous Status
CS - Current Status
If some spec status is different between current and previous run, the formatter outputs previous status, current status and spec description. '.' stands for passed specs, 'F' for failed and 'P' for pending.
The code is far from perfect, so feel free to criticize and change it as you want.
Hope this helps. Let me know if you have any questions.