Got this:
use Lingua::En::Titlecase:from<Perl5>;
# this line is straight from doc
my $tc = Lingua::EN::Titlecase.new("CAN YOU FIX A TITLE?");
Get this:
Could not find symbol ''&Titlecase'' in ''GLOBAL::Lingua::EN''
As I recall, Inline::Perl5 worked for me when I kicked its tires about a month ago. Not sure what I'm doing wrong. Docs didn't shed any light on things for me
Could not find symbol ''&Titlecase'' in ''GLOBAL::Lingua::EN''
The reason for the error is that you used Inline::Perl5 with perl module Lingua::En::Titlecase which does not exist. You need a captial "N" in "EN":
use Lingua::EN::Titlecase:from<Perl5>;
my $tc = Lingua::EN::Titlecase.new("CAN YOU FIX A TITLE?");
say $tc;
Output:
Can You Fix a Title?
Related
When running srb init in a Rails app I get the following:
Generating /tmp/d20220723-3779490-paqj5l/reflection.rbi with 6784 modules and 142 aliases
Printing your code's symbol table into /tmp/d20220723-3779490-paqj5l/from-source.json
/home/allan/.asdf/installs/ruby/3.1.0/lib/ruby/gems/3.1.0/gems/sorbet-0.5.10206/lib/hidden-definition-finder.rb:123:in `write_constants': Your source can't be read by Sorbet. (RuntimeError)
You can try `find . -type f | xargs -L 1 -t bundle exec srb tc --no-config --isolate-error-code 1000` and hopefully the last file it is processing before it dies is the culprit.
If not, maybe the errors in this file will help: /tmp/d20220723-3779490-paqj5l/from-source.json.err
When I check that error file I find this:
Exception::raise(): Unimplemented Parser Node: EmptyElse
Is there a workaround to get past this error?
Anytime you see Exception::raise in a Sorbet error message, it means there was a bug in Sorbet. You can report Sorbet bugs at https://github.com/sorbet/sorbet/issues
I have created a fix for this bug here: https://github.com/sorbet/sorbet/pull/6161
It will require upgrading Sorbet before you can take advantage of the fix. If you can't wait for that, you will have to hunt down the file in your codebase that uses Ruby's new case ... in syntax for pattern matching with an empty else keyword, and either delete the else keyword or change it to mention else nil instead.
Sorry for the inconvenience.
In the future, please use https://github.com/sorbet/sorbet/issues to report all issues—I only happened to see this by accident today, but I normally do not monitor StackOverflow for bug reports.
For example, if I have a pipe function:
def process_data(weighting, period, threshold):
# do stuff
Can I get autocompletion on the process data arguments?
There are a lot of arguments to remember and I would like to make sure they get passed in correctly. In ipython, the function can autocomplete to show me the keyword args which is really neat, but I would like it to do this when piping a pandas dataframe too!
I don't see how this would be possible, but then again, I'm truly in awe of ipython and all its greatness. So, is this possible? If not, are there other hacks that people have come up with?
Install the pyreadline library.
$ pip install pyreadline
Update:
It seems like this problem is specific to some versions of ipython. The solution is the following:
Run below command from the terminal:
$ ipython profile create
It will create a default profile at ~/.ipython/profile_default/ipython_config.py
Now edit this ipython_config.py and add the below lines and it will solve the issue.
c = get_config()
c.Completer.use_jedi = False
Reference:
https://github.com/jupyter/notebook/issues/2435
https://ipython.readthedocs.io/en/stable/config/intro.html
I have the question about the proper handling of the config file. I'm trying to solve my issue for a couple of days now but with the best will, I just can't find out how to do it. I know that this question is maybe quite similar with all the others here and I really tried to use them - but I didn't really get it. I hope that some things about how snakemake works will be more clear when I solved this problem.
I'm just switching to snakemake and I thought I just can easily convert my bash script. To get familiar with snakemake I started trying a simple Data-Processing pipeline. I know I could solve my case while defining every variable within the snakefile. But I want to use an external config file.
First is to say, for better understanding I decided just to post the code which I thought would work somehow. I already played around with different versions for a "rule all" and the "lambda" functions, but nothing worked so far and it just would be confusing. I'm really a bit embarrassed and confused about why I can't get this working. The variable differs from the key because I aways had a version where I redefine the variable, like:
$ sample=config["samples"]
I would be incredibly thankful for an example code.
What I'd like to have is:
The config file:
samples:
- SRX1232390
- SRX2312380
names:
- SomeData
- SomeControl
adapters:
- GATCGTAGC
- GATCAGTCG
And then I thought I can just call the keys like different variables.
rule download_fastq:
output:
"fastq/{name}.fastq.gz"
shell:
"fastq-dump {wildcards.sample} > {output}"
later there will be more rules, so I thought for them I also just need a key:
rule trimming_cutadapt:
input:
"fastq/{name}.fastq"
output:
"ctadpt_{name}.fastq"
shell:
"cutadapt -a {adapt}"
I also tried something with a config file like this:
samples:
Somedata: SRX1232131
SomeControl: SRX12323
But in the end I also didn't find the final solution nor would I know how to add a third "variable" then.
I hope it is somehow understandable what I want to have. It would be very awesome if someone could help me.
EDIT:
Ok - I reworked my code and tried to dig into everything. I fear my understanding lacks in connecting the things I read in this case. I would really appreciate some tips which will probably help me to understand my confusion.
First of all: Rather than try to download data from a pipeline I decided to do this in a config step. I tried out two different versions now:
Based on this answer I tried version one. I like the version with the two files. But I'm stuck in how to deal with the variables now in things like using them with the lambda function or everything where you normally would write "config["sample"]".
So my problem here is that I don't knwo ho to proceed or how the correct syntax is now to call the variables.
#version one
configfile: "config.yaml"
sample_file = config["sample_file"]
import pandas as pd
sample = pd.read_table(sample_file)['samples']
adapt = pd.read_table(sample_file)['adapters']
rule trimming_cutadapt:
input:
data=expand("../data/{sample}.fastq", name = pd.read_table(sample_file)['names']),
lambda wildcards: ???
output:
"trimmed/ctadpt_{sample}.fastq"
shell:
"cutadapt -a {adapt}"
So I went back to try to understand using and defining the wildcards. So (among other things) I looked into the example snakefile and the example rules of Johannes. And of course into the man. Oh and the Thing about the zip function.
At least I don't get an error anymore that it can't deal with wildcards or whatever. Now it's just doing nothing. And I can't find out why because I don't get any information. Additionaly I marked some points which I don't understand.
#version two
configfile: "config_ChIP_Seq_Pipeline.yaml"
rule all:
input:
expand("../data/{sample}.fastq", sample=config["samples"])
#when to write the lambda or the expand in a rule all and when into the actual rule?
rule trimming_cutadapt:
input:
"../data/{sample}.fastq"
params:
adapt=lambda wildcards: config[wildcards.sample]["adapt"] #why do I have to write .samle? when I have to use wildcard.XXX in the shell part?
output:
"trimmed/ctadpt_{sample}.fastq"
shell:
"cutadapt -a {params.adapt}"
As a testfile I used this one.
My configfile in version 1:
sample_file: "sample.tab"
and the tab file:
samples names adapters
test_1 input GACCTA
and the configfile from version two:
samples:
- test_1
adapt:
- GTACGTAG
Thanks for your help and patients!
Cheers
You can look at this post to see how to store and access sample information.
Then you can look at Snakemake documentation here, more specifically at the zip function, which might help you as well.
I have a variable
android="/media/New Volume_/android-sdk-linux_86"
I get an error saying that it cannot find the directory
I changed it to android="/media/New\ Volume_/android-sdk-linux_86"
I still get the same error. I even tried
android="/media/'New Volume_'/android-sdk-linux_86"
and I am using "$android" everywhere ...
I am not able to find the error, can someone help me..
Thanks
Take it this is bash? You assign variables with spaces like this:
android="/media/New Volume_/android-sdk-linux_86"
(Note you don't use the $ notation when setting a value.)
And reference them like this:
cd "$android"
I hate Xcode 4! It crashes all the time and finally it gives me an error in CABase.h file which is an library header file that I am not allowed to modify..
I don't even know how this file is broken.
How to fix this problem? It complains like
"Expected *before*
Expected '=',',',';','asm' or '_attribute_' before 'extern'
Also, how can I completely remove Xcode on my Mac and re-install?
You probably just have a simple error, perhaps in a header which is included prior to CABase.h. Use a "divide and conquer" strategy to locate it.
To answer your last question:
$ sudo /Developer/Library/uninstall-devtools –mode=all
This happened to me just because I had the letter 's' at the beginning of one of my implementation files. I must have missed the cmd key when cmd+s for saving the file. Luckily, another compile error discovered this and removing the 's' fixed both errors.
For example,
s//
// GraphingViewController.m