Re: [julia-users] Re: How to built an array with some keys of a dictionary ?

Thank you Dan, this solution works to ! I don't know which one is better :) Le mardi 8 novembre 2016 08:40:37 UTC+1, Dan a écrit : > > I meant, > > a = Vector{String}() > >

Re: [julia-users] Re: How to built an array with some keys of a dictionary ?

Thank you very much Mauro, that was the mistake ! :) > Array{String}(0) > > works. The other creates a zero-dimensional vector (just like a scalar) > to which you cannot push. > > > julia> a = Array{String}() > > WARNING: Base.String is deprecated, use AbstractString instead. > > likely

[julia-users] Re: How to built an array with some keys of a dictionary ?

Hi Steven, I also tried a = Array{String}() unfortunately it produces errors as well. julia> a = Array{String}() WARNING: Base.String is deprecated, use AbstractString instead. likely near no file:0 0-dimensional Array{AbstractString,0}: #undef julia> for k in keys(dict) if

[julia-users] How to built an array with some keys of a dictionary ?

Hi, I have many problems to build arrays with the keys of a dictionary except for the simple situation : a = [uppercase(key) for key in keys(dict)]# works fine If I try to select the keys with more complex criteria like : dict = Dict("a" => 1, "b" => 2, "c" => 3, "d" => 4, "e" => 5) a =

[julia-users] Re: How to stop program execution at some point

Yes Michele, "die" is able to stop execution at any point, even outside a loop, this is what I searched and did not found in Julia.

[julia-users] How to stop program execution at some point

Hi, I search in Julia the equivalent of Perl die; to stop the execution of a program. I tried "break" but it produces an error : ERROR: LoadError: syntax: break or continue outside loop I did not found "stop" as well. Thanks !

[julia-users] Re: Writing a subset DataFrame to file is 220 times slower than saving the whole DataFrame

Wow ! Impressive difference, it is 100 time faster without sub() : s = df[df[:rank_PV].<=r_max,:] @time write_results(s, name, "significant", sep, h) Saving... significant/Stat.csv 0.704880 seconds (7.14 M allocations: 164.687 MB, 2.40% gc time) s = sub(df, (df[:rank_PV] .<= r_max)) @time

[julia-users] Writing a subset DataFrame to file is 220 times slower than saving the whole DataFrame

Hi, In the same program, I save in a file a DataFrame "df" and a subset of this DataFrame in another file. The problem I have is that saving the subset is much slower than saving the entire DataFrame : 220 times slower. It is too slow and I don't what is my mistake. Thank you for your

Re: [julia-users] How to determine the type of a complex data structure

Hi ! Here are the results : type Ions_frag{} mz::Float64 intensity::Float64 charge::Int64 end computation time : 26.88 s immutable Ions_frag mz::Float64 intensity::Float64 charge::Int64 end computation time : 27.00 s Ions = Dict{ASCIIString, Ions_frag}() immutable

Re: [julia-users] How to determine the type of a complex data structure

Thank you very much Yichao, I will try : Dict{Any,Ions_frag} and immutable Ions_frag mz::Float64 intensity::Float64 charge::Int64 end

Re: [julia-users] How to determine the type of a complex data structure

Thank you very much Yichao, Tim and Jeffrey for your answers ! I try to summarize. If I understand well, this type definition is correct and gives the maximum performances : type Ions_frag mz::Float64 intensity::Float64 charge::Int64 end But if I use : d = Dict() d["key1"] =

Re: [julia-users] How to determine the type of a complex data structure

yStillAmbiguousType a::AbstractFloat end Le mardi 12 juillet 2016 17:32:09 UTC+2, Yichao Yu a écrit : > > On Tue, Jul 12, 2016 at 11:10 AM, Fred <fred.so...@gmail.com > > wrote: > > I am referring to all 3, ie the type of Ions_frag :) > > Well, can you qu

Re: [julia-users] How to determine the type of a complex data structure

ons_frag variables appropriately initialized with > mz, intensity, charge; and then uses them as they are. > > On Tuesday, July 12, 2016 at 11:10:40 AM UTC-4, Fred wrote: >> >> I am referring to all 3, ie the type of Ions_frag :) >> Initially I used : >>

Re: [julia-users] How to determine the type of a complex data structure

I am referring to all 3, ie the type of Ions_frag :) Initially I used : type Ions_frag mz::Float64 intensity::Float64 charge::Int64 end and it works. But, after reading the documentation I "understood" that it is not optimal in performances. Le mardi 12 juillet 2016 16:59:57 UTC+2,

[julia-users] How to determine the type of a complex data structure

Hi, I have a this kind of data structure : type Ions_frag{} mz::Float64 intensity::Float64 charge::Int64 end I read in performance tips that it is better to define the type of the data structure but I cannot find the good one for my data structure. I tried : type Ions_frag{DataType}

[julia-users] Re: changing record separator to read text files

It works using "" instead of '' ! Thanks ! julia> readuntil(f, "CKV\n") "\nTA\n>sp|P30464|1B15_HUMAN HLA class I histocompatibility antigen, B-15 alpha chain OS=Homo sapiens GN=HLA-B PE=1

[julia-users] Re: changing record separator to read text files

Thank you very much Dan ! Indeed readuntil works much better. But it seems to accept only one end line character. Is it possible to use a more complex pattern ? julia> readuntil(f, '>') "sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1

[julia-users] changing record separator to read text files

Hi ! It is often very useful to read a text files by blocks of lines, using another line separator than '\n'. Especially in bio-informatics, for example DNA or Protein FASTA sequences are separated by '\n>' (see uniprot.txt attached). In Perl, it is possible to change the line separator

[julia-users] Re: How can I find the common elements of two matrix(or arrays)?

julia> a=[1,3,5,7] 4-element Array{Int64,1}: 1 3 5 7 julia> b=[2,3,5,6,7] 5-element Array{Int64,1}: 2 3 5 6 7 julia> intersect(a,b) 3-element Array{Int64,1}: 3 5 7 julia> union(a,b) 6-element Array{Int64,1}: 1 3 5 7 2 6 Le lundi 4 juillet 2016 04:18:10 UTC+2, siyu song a

[julia-users] Re: How can I find the common elements of two matrix(or arrays)?

intersect(a,b) union(a,b) Le dimanche 3 juillet 2016 19:54:02 UTC+2, siyu song a écrit : > > In MATLAB, it's easy to do this by using : find(Mat_a == Mat_b). Is there > an easy similar way to do this? >

[julia-users] Re: ArrayFire.jl - GPU Programming in Julia

require at ./loading.jl:259 while loading /home/fred/.julia/v0.4/ArrayFire/src/config.jl, in expression starting on line 6 while loading /home/fred/.julia/v0.4/ArrayFire/src/ArrayFire.jl, in expression starting on line 5

[julia-users] Re: DataFrame : aggregate with only on column possible ?

Thank you Cédric ! Yes it works with an extra column a_1 : julia> df 8x4 DataFrames.DataFrame │ Row │ a │ b │ c │ sum│ ┝━┿━━━┿━━━┿━━━┿┥ │ 1 │ 1 │ 2 │ 2.28386 │ -0.0551961 │ │ 2 │ 2 │ 1 │ 0.174953 │ 0.472804 │ │ 3 │ 3 │ 2 │ -1.31137 │ 0.994803

[julia-users] Re: DataFrame : aggregate with only on column possible ?

Thank you Cedric ! To clarify I give you an example : │ Row │ a │ b │ c│ sum │ ┝━┿━━━┿━━━┿━━┿━┥ │ 1 │ X │ 2 │ 10 │12 │ │ 2 │ Y │ 1 │ 3│ 4 │ │ 3 │ Z │ 2 │ 5│ 7 │ │ 4 │ X │ 1 │ 20 │ 21 │ │ 5 │ X │ 2 │ 5│ 7 │ │ 6 │ Z │ 1 │ 8│ 9 │ I want

[julia-users] DataFrame : aggregate with only on column possible ?

Hi, I have a dataframe df2 and the last column is the sum = b+c : julia> df2 8x4 DataFrames.DataFrame │ Row │ a │ b │ c │ sum │ ┝━┿━━━┿━━━┿━━━┿━━━┥ │ 1 │ 1 │ 2 │ -0.163564 │ 1.83644 │ │ 2 │ 2 │ 1 │ 0.731038 │ 1.73104 │ │ 3 │ 3 │ 2 │ 0.0951149 │

[julia-users] replacing "require" by "include" does not import DataFrames

Hi ! I have a old parallel program that works perfectly with "require" and I can't manage to make it work with "include". The reason I try to do that is that "require" is deprecated. old program that worked : main : require("file.jl") pmap(function, list_of_dataframes) file.jl : using

[julia-users] Re: parallel computing in julia

To start 4 cpus : $ julia -p 3 _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_)| Documentation: http://docs.julialang.org _ _ _| |_ __ _ | Type "?help" for help. | | | | | | |/ _` | | | | |_| | | | (_| | | Version 0.4.5

[julia-users] Re: parallel computing in julia

Hi, You have started julia and then you try to start it again with julia -p 2. just type julia -p 2 in a terminal before starting julia :) $ julia -p 2 _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_)| Documentation:

Re: [julia-users] Creating an empty 2D array and append values to it

Thank you ! I think I will use this solution : julia> a = [] 0-element Array{Any,1} julia> b = [] 0-element Array{Any,1} julia> push!(a, 1) 1-element Array{Any,1}: 1 julia> push!(a, 2) 2-element Array{Any,1}: 1 2 julia> a 4-element Array{Any,1}: 1 2 3 4 julia> b 4-element

Re: [julia-users] Creating an empty 2D array and append values to it

ulting `A = [c1 c2]`. > > On Tuesday, April 12, 2016 at 10:38:41 AM UTC-4, Fred wrote: >> >> Thank you very much Tim ! >> >> In fact I want to create an X,Y array so if I create a 1D array, I can >> only append to it (x1,y1) then (x2,y2)... (xn, yn), because I cal

Re: [julia-users] Creating an empty 2D array and append values to it

Thank you very much Tim ! In fact I want to create an X,Y array so if I create a 1D array, I can only append to it (x1,y1) then (x2,y2)... (xn, yn), because I calculate x1 before x2... julia> d = ["x1", "y1", "x2", "y2", "x3", "y3"] 6-element Array{ASCIIString,1}: "x1" "y1" "x2" "y2" "x3"

Re: [julia-users] Creating an empty 2D array and append values to it

Thank you very much Yichao ! This explain all the problems I have... But it still unclear : I cannot create an empty 1D array and resize it : julia> b = Array[] 0-element Array{Array{T,N},1} julia> b = Array[] 0-element Array{Array{T,N},1} julia> reshape(b,2,2) ERROR: DimensionMismatch("new

[julia-users] Creating an empty 2D array and append values to it

Hi ! The questions I have is so trivial that I spend a long time trying to find an example on the doc and on the web but I did not manage to do exactly what I want : I want to create an empty 2D array : the function readdlm create exactly the kind of array I want if I read a CSV file with 2

[julia-users] Re: Find the indice of the element with the nearest value of a float in an array

Thank you for this explanation DNF ! It is the first time I use collect and the reason why I used it was an error message suggesting that I should use it :) maybe because of my first mistake to use []. Le dimanche 10 avril 2016 23:30:10 UTC+2, DNF a écrit : > > The big error you made

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

A huge size difference ! I have to read my array from data file so I suppose it is like Y and X is only for simulations ? Le dimanche 10 avril 2016 17:50:02 UTC+2, Tim Holy a écrit : > > Just FYI: > > julia> x = 1:0.1:100 > 1.0:0.1:1.0e6 > > julia> y = collect(x); # this is the same as y

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

Maybe my array is too small to see a difference, but if I increase the size I will lack of RAM ;) julia> x = 1:0.1:100 1.0:0.1:1.0e6 julia> @time searchsorted(x, 8.22) 0.045590 seconds (33.21 k allocations: 1.535 MB) 74:73 julia> @time searchsorted(x, 8.22) 0.05 seconds (8

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

Hi, I post here my best solution taking advantage that the array is sorted. I expected that solution to be a lot much faster than other solutions, but not really. Indeed I am very impressed by the speed of searchsorted : x = [1:0.1:100] val = 8.22 function dicotomy(x, val) a =

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

Hi, I post here my best solution taking advantage that the array is sorted. I expected to be a lot much faster than other solutions, but not really. I am very impressed by the speed of searchsorted : x = [1:0.1:100] val = 8.22 function dicotomy(x, val) a = start(eachindex(x)) b =

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

That's true ! But why a loop is faster in a function ? :) > > I seem to recall that your example loop was not in a function(?) If so, > that makes it lots slower. > >

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

I tested my loop monre than 2 times as it is written in my post and I have always the same results. The function Tim Holy posted is much faster, I posted the results above :) > Probably you are doing this wrong; it shouldn't be allocating so much > memory. Is your loop using global

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

Thank you very much Mauro ! searchsorted is the simplest solution and one of the fastest but it gives two indices so another comparison is needed to find the closest value : @time searchsorted(x, 8.22) 0.04 seconds (7 allocations: 240 bytes) 74:73 abs(x[73] - 8.22) > abs(x[74] - 8.22)

Re: [julia-users] Find the indice of the element with the nearest value of a float in an array

Thank you very much ! I give you the results : my loop solution : 0.000419 seconds (547 allocations: 708.797 KB) 0.02135 -> 73 @time closest_index(x,8.22) 0.03 seconds (4 allocations: 160 bytes) 73 @time for (i,x) in enumerate(array)... 0.000181 seconds (821 allocations:

[julia-users] Find the indice of the element with the nearest value of a float in an array

Hi, I am looking for the most efficient (fastest) way to find the indice of the element with the nearest value of a float in an array. x = [1:0.1:10] julia> x 91-element Array{Float64,1}: 1.0 1.1 1.2 1.3 1.4 ⋮ 9.4 9.5 9.6 9.7 9.8 9.9 10.0 It is very easy to find the

[julia-users] Re: Read External file data

Hi, Of course it is possible : https://en.wikibooks.org/wiki/Introducing_Julia/Working_with_text_files You can read data frames to : https://dataframesjl.readthedocs.org/en/latest/io.html

Re: [julia-users] SharedArray returns unexpected empty values

Thank you ! I will try on a more complex example ;)

Re: [julia-users] SharedArray returns unexpected empty values

I compared the speed of the parallel loop : it is 10 times slower (with 4 cpus) than the simple loop :( @time @sync @parallel for i=1:80 c[i] = prod(a[i], b[i]) end #println(c) @time for i=1:80 c[i] = prod(a[i], b[i]) end 0.728079 seconds (391.50 k allocations: 16.659 MB) 0.091947

[julia-users] SharedArray returns unexpected empty values

Hi, I did this simple code to try to understand how shared arrays work. Unfortunately my shared array c[ ] is always empty :( Here I know the size of the final array c because it is a very simple example, but is it possible to create an empty shared array and push the results inside using

Re: [julia-users] How to copy a DataFrame structure in an empty DataFrame

Thank you tshort. Is there a website or email address to post requests concerning documentation ? Le jeudi 24 mars 2016 19:28:44 UTC+1, tshort a écrit : > > Feel free to file issues for missing documentation or (even better) pull > requests. > >

Re: [julia-users] How to copy a DataFrame structure in an empty DataFrame

Thank you Milan for this useful link. This website contains more informations than mine, but it does not seems to contains all the functions available for dataframes. For example I did not manage to find that I have to use append! instead of push! to add a row to a dataframe.

Re: [julia-users] How to copy a DataFrame structure in an empty DataFrame

Thank you very much Milan ! When I searched a solution in DataFrame documentation I did not found the keyword "similar". Is there an equivalent for Julia of this website for Perl for example ? julia> df = readtable("test2.tsv") 4x4

[julia-users] How to copy a DataFrame structure in an empty DataFrame

Hi, I have a DataFrame "df" and I would like to create a new DataFrame "m" with the same colnames than df. And then, append to "m" the rows of "df" matching a complex set of conditions, so I need to test many conditions for each row. The problem I have is to create an empty dataframe "m"

[julia-users] Julia : install problem on ubuntu : Signing key not available

without a GPG key problem ? Thanks in advance ! Fred

Re: [julia-users] One click execution of Julia program

That's true, it seems to be related to the system. On my system, lightweight (XFCE), a double click open any executable Julia program in a text editor and I don't have the choice to execute in a terminal. But, if I run the program in a terminal using ./program.jl it works, indicating that the

Re: [julia-users] One click execution of Julia program

.jl" instead of "*" Le jeudi 7 janvier 2016 10:51:29 UTC+1, Fred a écrit : > > I solved the problem :) > > In XFE (http://roland65.free.fr/xfe/) associate .jl files > with /usr/bin/julia allows one click execution of Julia programs :) > In Thunar, it seems to be much

Re: [julia-users] One click execution of Julia program

I solved the problem :) In XFE (http://roland65.free.fr/xfe/) associate .jl files with /usr/bin/julia allows one click execution of Julia programs :) In Thunar, it seems to be much more difficult : https://bbs.archlinux.org/viewtopic.php?id=194464 Le jeudi 7 janvier 2016 10:29:57 UTC+1, Fred

[julia-users] One click execution of Julia program

Hi ! I would like to know if it is possible to execute a julia program just by clicking on the program name on GNU/Linux (of course after a chmod +x program.jl). I manage to do that in bash using #!/usr/bin/bash or in Perl #!/usr/bin/perl but in Julia I try to insert the lines :

Re: [julia-users] One click execution of Julia program

Hi Abel on my system I have : $ which julia /usr/bin/julia Le mercredi 6 janvier 2016 19:06:13 UTC+1, Abel Siqueira a écrit : > > Julia is on `/usr/local/bin` in my system. Verify if the path is correct > with `which julia`. > Using the correct path I managed to run it on the terminal as

Re: [julia-users] Array of DataFrames

*Thanks Milan ! ;)* julia> using DataFrames julia> sep = '\t' '\t' julia> data = DataFrame[] 0-element Array{DataFrames.DataFrame,1} > The problem is in this line, which creates an array of arrays of data > frames. It should simply be > DataFrame[] > or even > [] > given that

[julia-users] Array of DataFrames

call{T}(::Type{T}, ::Any) convert(::Type{DataFrames.DataFrame}, ::Array{T,2}) convert(::Type{DataFrames.DataFrame}, ::Dict{K,V}) ... in setindex! at array.jl:313 in copy! at abstractarray.jl:344 in copy! at abstractarray.jl:326 in convert at /home/fred/.julia/v0.4/DataFrames/s

Re: [julia-users] DataFrames : Apply a function by rows

Yes, it is a good solution, but it means that DataFrames cannot be used to do some calculations by rows, it is a severe limitation. An equivalent of colwise() whould be very usefull. Le dimanche 22 novembre 2015 14:11:21 UTC+1, tshort a écrit : > > I'd convert the whole DataFrame to a matrix

Re: [julia-users] DataFrames : Apply a function by rows

Ok, I hope that exchange could contribute to bring news ideas to improve DataFrames although there are other way to do it, like convert a DataFrame or a row into array. Thank you for your help ! Le dimanche 22 novembre 2015 15:48:37 UTC+1, tshort a écrit : > > Contributions/pull requests from

Re: [julia-users] DataFrames : Apply a function by rows

It is a good idea but how is it possible to iterate two dataframes at the same time ? Something like : julia> df = DataFrame(a=1:5, b=7:11, c=10:14, d=20:24) 5x4 DataFrames.DataFrame | Row | a | b | c | d | |-|---|||| | 1 | 1 | 7 | 10 | 20 | | 2 | 2 | 8 | 11 | 21 | | 3

Re: [julia-users] DataFrames : Apply a function by rows

> You can try `eachrow`. It probably won't be fast, though. Here's an > example: > > > https://github.com/JuliaStats/DataFrames.jl/blob/master/test/iteration.jl#L34 > On Nov 21, 2015 7:19 AM, "Fred" <fred.so...@gmail.com > > wrote: > >> Hi,

Re: [julia-users] DataFrames : Apply a function by rows

like : julia> for r1,r2 in eachrow(df1, df2) println(TTest(r1,r2)) end ERROR: syntax: invalid iteration specification Le samedi 21 novembre 2015 19:17:27 UTC+1, Fred a écrit : > > It is a good idea but how is it possible to iterate two dataframes at the &g

Re: [julia-users] How to use variables in subsets of DataFrames ?

Great answer Rob ! This is exactly what I was looking for ! Many Thanks ! Fred Le lundi 28 septembre 2015 17:35:15 UTC+2, Rob J Goedman a écrit : > > Fred, > > Would below example work for you? > > *julia> **dft = readtable("/Users/rob/Desktop/test.csv"

[julia-users] How to use variables in subsets of DataFrames ?

Hi ! I would like to know how is it possible to use variables in subsets of DataFrames ? I would like to use a syntax like df[:,:titles[1]] and df[:,:titles[1:3]] Thanks for your help ! julia> using DataFrames julia> df = readtable("test.csv", separator = '\t') 8x5 DataFrame | Row | title1

[julia-users] Re: How to know the size of a large array stored in a csv file (greater than RAM

If you use GNU/Linux or Unix you can obtain the number of lines with : wc -l file.csv Le dimanche 14 juin 2015 09:51:29 UTC+2, paul analyst a écrit : How to know the size of a large array stored in a csv file (greater than RAM, I can not use readcsv. After that I want to apply the open

[julia-users] Julia parallel when number of tasks number of CPUs

Hi ! When the number of tasks exceed the number of CPUs, is it safe to send all the tasks in pmap() function ? For example, if I have 20 tasks and 4 CPUs, can I use the command : pmap(function,[var1, var2,var20]) Or is there a way to tel pmap() to process the task 4 by 4 ? Thanks ! ;)

[julia-users] trying to do a simple parallel program with Julia

-001.jl exception on 3: ERROR: opening file tab2csv: Aucun fichier ou dossier de ce type in open at ./iostream.jl:117 in open at ./iostream.jl:125 in readtable at /home/fred/.julia/v0.3/DataFrames/src/dataframe/io.jl:889 in process_table at /archives/logiciels/julia/parallel-05.jl:7

[julia-users] Re: trying to do a simple parallel program with Julia

Hi ! I found the bug : a dot was missing in pmap(process_table,{tab.csv,tab2csv}) instead of pmap(process_table,{tab.csv,tab2.csv}) The program works perfectly, I have to change my glasses 8-)