I tried to import System.Directory in my Frege program (In Eclipse) in order to use functions as getDirectoryContent, etc., and it writes me this error :
Could not import module frege.system.Directory (java.lang.ClassNotFoundException: frege.system.Directory)
What do I have to do ?
It is because the module frege.system.Directory doesn't exist in Frege. A good way to find out about a module is to use Hoogle for Frege at this URL: http://hoogle.haskell.org:8081. If we search for that module there, we can see that it doesn't list any module as opposed to, say, if you search for frege.data.List, we would see the module in the result.
Now for the functions you need like getDirectoryContent, if you look at the search result for frege.system.Directory, the first result is about processes and the third and fourth results are about jars and zip files. If you click on the second result, it would open the module frege.java.IO and you can see some relevant functions that might be useful for you (list for example). However the Haskell module you are trying to find is not yet ported to Frege but it should, of course, be possible to port that module backed by native Java implementations.
Update for OP's comment
Here is a simple snippet to return the files under a given directory:
ls :: String -> IO [String]
ls dir = do
contents <- File.new dir >>= _.list
maybe (return []) (JArray.fold (flip (:)) []) contents
Regarding createTempFile, the following works for me:
frege> File.createTempFile "test.txt"
String -> STMutable RealWorld File
Related
I just sat down to write my first Nim script to parse a .vcf (Variant Call Format) file. This file format stores genetic mutations from sequencing data.
For scripting languages, I 'grew up' on Perl and later migrated to Python, but I would love to use a language with the speed that Nim offers. I realize Nim is still young, but I couldn't even find a clear example for how to open and read a .gz (gzip) file (preferably line by line).
Can anyone provide a simple example to open and read a gzip file using Nim, line by line?
In Python, I'm accustomed to the following (uber-simple) code:
import gzip
my_file = gzip.open('my_file.vcf.gz', 'w')
for line in my_file:
# do something
my_file.close()
I have seen related questions, but they're not clear. The posts are also relatively old and I hope/suspect something better has come about. Here's what I've found:
Read gzip-compressed file line by line
File, FileStream, and GZFileStream
Reading files from tar.gz archive in Nim
Really appreciate it.
P.S. I also think it would be useful if someone created a Nim tag in StackOverflow. I do not have the reputation to create tags.
Just in case you need to handle VCF rather than .gz, there's a nice wrapper for htslib written by Brent Pedersen:
https://github.com/brentp/hts-nim
You need to install the htslib in your system, and then require the library in your .nimble file with requires "hts", or install the library with nimble install hts. If you are going to do NGS analysis in Nim you'll need it.
The code you need:
import hts
var v:VCF
doAssert open(v, "myfile.vcf.gz")
# Here you have the VCF file loaded in v, and can access the headers through
# v.header property
for record in v:
# Here you get a Record object per line, e.g. extract the Ref and Alts:
echo v.REF, " ", v.ALT
v.close()
Be sure to follow the docs, because some things differ from python, specially when getting the INFO and FORMAT fields.
Checkout the whole Brent repo. It has plenty of wrappers, code samples and utilities to handle NGS problems (e.g. an ultrafast coverage tool utility called Mosdepth).
Per suggestion from Maurice Meyer, I looked at the tests for the Nim zip package. It turned out to be quite simple. This is my first Nim script, so my apologies if I didn't follow convention, etc.
import zip/gzipfiles # Import zip package
block:
let vcf = newGzFileStream("my_file.vcf.gz") # Open gzip file
defer: outFile.close() # Close file (like a 'final' statement in 'try' block)
var line: string # Declare line variable
# Loop over each line in the file
while not vcf.atEnd():
line = vcf.readLine()
# Cure disease with my VCF file
To install the zip package, I simply ran because it is already in the Nim package library:
> nimble refresh
> nimble install zip
I tried to use Nim some time ago to parse a fastq or fastq.gz file.
The code should be available here:
https://gitlab.pasteur.fr/bli/qaf_demux/blob/master/Nim/src/qaf_demux.nim
I don't remember exactly how this works, but apparently, I did an import zip/gzipfiles and used newGZFileStream on the input file name to obtain a Stream from which lines can be read using .readLine() in this piece of code:
proc fastqParser(stream: Stream): iterator(): Fastq =
result = iterator(): Fastq =
var
nameLine: string
nucLine: string
quaLine: string
while not stream.atEnd():
nameLine = stream.readLine()
nucLine = stream.readLine()
discard stream.readLine()
quaLine = stream.readLine()
yield [nameLine, nucLine, quaLine]
It is used in something that amounts to this piece of code:
let inputFqs = fastqParser(newGZFileStream($inFastqFilename))
Hopefully you can adapt this to your case.
My .nimble file has a requires "zip#head". I suppose this triggers the installation of zip/gzipfiles.
I am a little confused about how to structure a go web app and its tests. I have read the How to Write Go Code but still don't get it. For example, I have a go project called "beacon" with a beacon.go file at the root. Adding a trivial beacon_test.go file (copied verbatim from http://golang.org/pkg/net/http/httptest/#example_Server) causes this error:
$ go test
# github.com/jelder/beacon
./beacon_test.go:11: main redeclared in this block
previous declaration at ./beacon.go:216
FAIL github.com/jelder/beacon [build failed]
Sure enough, line 11 is func main(). If I instead change the package main line in my beacon_test.go to package hello, I get this error instead:
can't load package: package github.com/jelder/beacon: found packages main (beacon.go) and hello (beacon_test.go) in /Users/jacob/src/github.com/jelder/beacon
beacon_test.go has also a function called main() rename it to TestFirst (or any other name you like as long as it starts with Test, note the uppercase T is important). There is no need for that. Just run go test . from inside the package you are working on (the one containing the *.go files). Post the full files if you need more help.
I am new to stackoverflow, but I got a lot of help until now, thanks to the community for that.
I'm trying to create a software showing me caller depandencys for legacycode.
I'parsing a directory with c code with pycparcer, and for each file i want to create a subgraph with pydot.
Two questions:
When parsing a c file, the parser references the #includes, an i get also functions in my AST, from the included files. How can i know, if the function is included, or originaly from this actual file/ or ignore the #includes??
For each file i want to create a subgraph, an then add all functions in this file to this subgraph. I don't know how many subgraphs i have to create...
I have a set of files, where each file is a frozenset with the functions of this file
somthing like this is pssible?
for files in SetOfFiles:
#how to create subgraph with name of files?
for function in files:
self.graph.add_node(pydot.Node(funktion)) #--> add node to subgraph "files"
I hope you got my challange... any ideas?
Thanks!
EDIT:
I solved the question about pydot, it was quiet easy... So I stay with my pycparser problem :(
for files in ListOfFuncs:
cluster_x = pydot.Cluster(files, label=files)
for functions in files:
cluster_x.add_node(pydot.Node(functions))
graph.add_subgraph(cluster_x)
I can address the pycparser part. The preprocessor leaves #line directives that specify which file & line code came for, and pycparser consumes those. You can get that information from the AST it creates (see tests for an example).
I know this question came up in similar variations often, but no solution seems to fully fit my needs. I have the following problem:
In development I use multiple JS files (a single file every "object"). These JS files have several dependencies within each other - some rely on others and I need to load them first. Currently I use RequireJS to load each JS file in the right order, so I define a module for each file. Fine and dandy.
But now I want to concatenate all my JS files into one big JS file which should be a module itself. I use the RequireJS optimizer r.js to do that. My problem: Every JS file is concatenated to a big JS file, but the module definition for each object is included to. I don't have one big module in one big file, but many modules in one big file.
After that I tried grunt for concatenating which works fine, but ignores dependencies of files. It just concatenates every file in alphabetical order or I have to hardcode the order in my gruntfile.
How can I solve this?
Just as an illustration to my problem:
I have following files (pseudo code):
FileA
- define FileA module
- depends on FileB
- FileA Logic
FileB
- define FileB module
- FileB Logic
And I want this output:
LibFile
- define LibFile module
- FileB Logic, FileA Logic
But I get this with r.js (module definition from FileA and FileB is copied):
LibFile
- define FileB module
- FileB Logic
- define FileA module
- depends on FileB
- FileA Logic
And I get this with grunt (wrong order):
LibFile
- FileA Logic
- FileB Logic
Maybe that questions is a little bit stupid, but I just can't solve this with the tools everybody seems to use...
I tried the grunt-requirejs plugin, too. But it throws several erros which I couldn't resolve.
Thank you,
Pipo
I am going to move it into an answer. Just so the code is a bit clearer.
I am doing these by memory (since I can't test it right now) so some little things may be not entirely accurate.
It depends of course on how you package your modules, but one way is to register all your smaller modules in a bigger module:
File A.js
define([], function() {
// do something
return A;
});
File B.js
define(['path/to/A'], function(A){
// do something with A and more
return B;
});
Then, you package them together:
File mylib.js
define(['path/to/A', 'path/to/B'], function(A, B){
return {
A : A,
B : B
}
}
you then can point your build profile to mylib.js and it will be combined into
one big file. It won't be one all-encapsulating module, but it will have an entry
module that references everything else. You then can use it like so:
require.config({
paths : {
'path/to/mylib' : 'real/path/to/mylib/on/server'
}
});
require(['path/to/mylib'], function(Lib) {
// do something using Lib.A or Lib.B
}
the one thing to pay attention to is the ID of your big module file. By default
RequireJS build gives ID that matches physical path (from appDir IIRC) and you
have to match that when you load your dependency. Simply put, if your resulting
mylib.js file has a main module that received the name 'path/to/mylib', you will
have to match it and load it by the same ID (using require.config.paths) or play with
maps and such (some of which requires RequireJS 2.0).
The following is the reason I asked you why would you want to do the "big module" thing
Other thing of note is that all your inner smaller modules also receive IDs matching their
physical path and you can use these IDs when you use the big package module (so that you can access them not only through Lib.A) if mylib.js has been loaded:
require(['path/to/A'], function(A) {
// do something using A
}
Does OCaml have a way to get the current file/module/script name? Something like:
C/C++'s argv[0]
Python's sys.argv[0]
Perl/Ruby's $0
Erlang's ?FILE
C#'s ProgramName.Environment.CommandLine
Factor's scriptname/script
Go's os.Args[0]
Haskell's System/getProgName
Java's System.getProperty("sun.java.command").split(" ")[0]
Node.js's __filename
etc.
I don't know anything about OCaml but some googling turned up
Sys.argv.(0)
See http://caml.inria.fr/pub/docs/manual-ocaml/manual003.html#toc12
I presume you are scripting in OCaml. Then Sys.argv.(0) is the easiest way to get the script name. Sys module also provides Sys.executable_name, but its semantics is slightly different:
let _ = prerr_endline Sys.executable_name; Array.iter prerr_endline Sys.argv;;
If I run the above line, putting the line in test.ml, by ocaml test.ml hello world, I have:
/usr/local/bin/ocaml - executable_name
test.ml - argv.(0)
hello - argv.(1)
world - argv.(2)
So OCaml toplevel does something fancy against argv for you.
In general, obtaining the current module name in OCaml is not easy, from several reasons:
ML modules are so flexible that they can be aliased, included into other modules, and applied to module functors.
OCaml does not embed the module name into its object file.
One probably possible workaround is to add a variable for the module name by yourself, like:
let ml_source_name = "foobar.ml"
This definition can be probably auto inserted by some pre-processing. However, I am not sure CamlP4 can have the file name of the currently processing source file.
If your main purpose is simple scripting, then of course this pre-processing is too complicated, I am afraid.
let _ =
let program = Sys.argv.(0) in
print_endline ("Program: " ^ program)
And posted to RosettaCode.
In OCaml >= 4.02.0, you can also use __FILE__ to get the filename of the current file, which is similar to Node's __filename and not the same as Sys.argv.(0).