I am using OCLint static code analysis tool for objective-C and want to find out how to customize rules? The rules are represented by set of dylib files.
In lieu of passing configuration as arguments (see Jon Boydell's answer), you can also create a YML file named .oclint in the project directory.
Here's an example file that customizes a few things:
rules:
- LongLine
disable-rules:
rulePaths:
- /etc/rules
rule-configurations:
- key: LONG_LINE
value: 20
output: filename
report-type: xml
max-priority-1: 10
max-priority-2: 20
max-priority-3: 30
enable-clang-static-analyzer: false
The answer, as with so many things, is that it depends.
If you want to write your own custom rule then you'll need to get down and dirty into writing your own rule, in C++ on top of the existing source code. Check out the oclint-rules/rules directory, size/LongLineRule.cpp is a simple rule to get going with. You'll need to recompile, etc.
If you want to change the parameters of an existing rule you need to add the command line parameter -rc=<rulename>=<value> to the call to oclint. For example, if you want the long lines rule to only activate for lines longer than 150 chars you need to add -rc=LONG_LINE=150.
I don't have the patience to list out all the different parameters you can change. The list of rules is here http://docs.oclint.org/en/dev/rules/index.html and a list of threshold based rules here http://docs.oclint.org/en/dev/customizing/rules.html but there's no list of acceptable values and I don't know whether these two URLs cover all the rules or not. You might have to look into the source code for each rule to work out how it works.
If you're using Xcode script you should use oclint_args like this:
oclint-json-compilation-database oclint_args "-rc LONG_LINE=150" | sed
's/(..\m{1,2}:[0-9]:[0-9]*:)/\1 warning:/'
in that sample I'm changing the rule of LONG_LINE to 150 chars
Related
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.
A number of commands produce silently extra files not defined in the rule output section.
When I try to make sure these are produced by adding them to 'rule all:' a re-run of the workflow fails because the file are not found in the rule(s) output list.
Can I add a supplementary file (not present as {output}) to the 'rule all:'?
Thanks
eg: STAR index produces a number of files in a folder defined by command arguments, checking for the presence of the folder does not mean that indexing has worked out normally
added for clarity, the STAR index exmple takes 'star_idx_75' as output argument and makes a folder of it in which all the following files are stored (their number may vary in function of the index type).
chrLength.txt
chrName.txt
chrNameLength.txt
chrStart.txt
exonGeTrInfo.tab
exonInfo.tab
geneInfo.tab
Genome
genomeParameters.txt
SA
SAindex
sjdbInfo.txt
sjdbList.fromGTF.out.tab
sjdbList.out.tab
transcriptInfo.tab
What I wanted was to check that they are all present BUT none of them is used to build the command itself and if I required them in the rule all: a rerun breaks because they are not in any snakemake {output} definition.
This is why I asked wether I could create 'fake' output variables that are not 'used' for running a command but allow placing the corresponding items in the 'rule all:' - am I more clear now :-).
Can I add a supplementary file (not present as {output}) to the 'rule all:'?
I don't think so, at least not without resorting on some convoluted solution. Every file in rule all (or more precisely the first rule) must have a rule that lists it in output.
If you don't want to repeat a long list, why not doing something like this?
star_index= ['ref.idx1', 'ref.idx2', ...]
rule all:
input:
star_index
rule make_index:
input:
...
output:
star_index
shell:
...
It's probably better to list them all in the rule's output, but only use the relevant ones in subsequent rules. You could also look into using directory() which could possibly fit here.
I'm struggling to integrate my sample sheet (TSV) into my pipeline. Specifically, I want to define the samples wildcard manually instead of reading it from a patch. The reason is that not all samples in a path are supposed to be analysed. Instead, I made a sample sheet that contains the list of samples, the path where to find, reference genome, etc.
The sheet looks like this:
name path reference
sample1 path/to/fastq/files mm9
sample2 path/to/fastq/files mm9
I load the sheet in my snakefile:
table_samples = pd.read_table(config["samples"], index_col="name")
SAMPLES = table_samples.index.values.tolist()
The first rule is supposed to merge the FASTQ files inside, so it would be nice to do something like this:
rule merge_fastq:
output: "{sample}/{sample}.fastq.gz"
params: path = table_samples['path'][{sample}]
shell: """
cat {params.path}/*.fastq.gz > {output}
"""
But as written above it won't work because the sample wildcard is not defined. Is there a way I can say the sample list I defined above (SAMPLES) contains all the samples for which rules should be executed?
I honestly feel stupid asking this question but I've already spent a couple of hours finding/searching a solution and at this point I need to be a bit more time efficient :D
Thanks!
You just need a target rule listing all the concrete files you want after your rule "merge_fastq":
rule all:
input: expand("{sample}/{sample}.fastq.gz",sample=SAMPLES)
This rule must be put at the top of the other rules. Wildcards can only be used if you define the concrete files you want at the end of the workflow.
This question is related to Swift and Objective-C.
I want to create variables from Constant Strings. So, in future, when I change name of a variable though out app, I just need to change it at one place, it must be changed, wherever it is used.
Example:
I have user_id in 14 files, if I want to change user_id into userID I have to change in all 14 files, but I want to change at once place only.
One way to do this would be to use the Xcode build process and add a script (language can be of your choice, but the default is a BASH script)
Create string constant text file where you define all your variables you want to change in some format that expresses the change you want to make, for example:
"variable_one_name" = "new_variable_one_name"
Depending on how 'smart' you wanted your script to be you could also list all your variables and include some way of indicating when a variable is not to be replaced.
"variable_one_name" = "new_variable_one_name"
"variable_two_name" = "DO_NOT_CHANGE"
Run a pre build script on you project that reads in the string constant text file and then iterates through your source files and executes the desired replacement. Be careful to limit the directories you search to you OWN source files!
build project...
This would allow you to manage your constants from one place. However it clearly is only going to help you after you have created a project and written some code :)
BASH string replacement
Adding a run script to the Xcode build process
Seems unlikely, but is there any way to generate a set of unit tests for the following rewrite rule:
RewriteRule ^/(user|group|country)/([a-z]+)/(photos|videos)$ http:/whatever?type=$1&entity=$2&resource=$3
From this I'd like to generate a set of urls of the form:
/user/foo/photos
/user/bar/photos
/group/baz/videos
/country/bar/photos
etc...
The reason I don't want to just do this once by hand is that I'd like the bounded alternation groups (e.g. (user|group|country)) to be able to grow and maintain coverage without having the update the tests by hand.
Is there a rewrite rule or regex parser that might be able to do this, or am I doing it by hand?
If you don't mind hacking a few lines of Perl then there's a package, Regexp::Genex that you can use to generate something close to what you require e.g.
# perl -MRegexp::Genex=:all -le 'print for strings(qr/\/(user|group|country)\/([a-z]+)\//)'
/user/dxb/
/user/dx/
/user/d/
/group/xd/
/group/x/
# perl -MRegexp::Genex=:all -le 'my $re=qr/\/(user|group|country)\/([a-z]+)\/(phone|videos)/;$Regexp::Genex::DEFAULT_LEN = length $re;print for strings($re)'
/user/mgcgmccdmgdmmzccgmczgmzzdcmmd/phone
/user/mgcgmccdmgdmmzccgmczgmzzdcmm/phone
/user/mgcgmccdmgdmmzccgmczgmzzdcm/phone
/user/mgcgmccdmgdmmzccgmczgmzzdc/phone
...
/group/gg/videos
/group/g/phone
/group/g/videos
/country/jvmmm/phone
/country/jvmmm/videos
/country/jvmm/phone
/country/jvmm/videos
/country/jvm/phone
/country/jvm/videos
/country/jv/phone
/country/jv/videos
/country/j/phone
/country/j/videos
#
Note:
1) You'll need to write a wrapper to parse the source file, tokenise (extract) the source patterns, escape certain characters in the rule e.g. "/", and possibly split your rules into more manageable parts, before expanding, via Genex, and then outputting the results, in the desired format.
2) To install the module type: cpan Regexp::Genex