as input for the script I have a list of BP ranges on several chromosomes and I am wondering how to write an IGV script that directly leads me only to these areas, without showing the whole chromosomes.
Thanks for your help in advance
Input:
Chr xy1 BP-start BP-end,
Chr xy1 BP2-start BP2-end,
Chr xy2 BP1-start BP1-end,
Chr xy2 BP2-start BP2-end,
Related
In Stata, after running the xthtaylor command, the command
matrix regtab = r(table)
yields an empty matrix. I think this is because of the multilevel of the output of this command
Being new to Stata, I haven't found how to fix this. The purpose here is to extract the coeffecient and standard errors to add them to another output (as is done in the accepted solution of How do I create a table wth both plain and robust standard errors?)
To expand on Nick's point: matrix regtab = r(table) gives you an empty matrix, because xthtaylor doesn't put anything into r(table).
To see this run the following example:
clear all // empties r(table) and everything else
webuse psidextract
* the example regression from `help xthtaylor`
xthtaylor lwage wks south smsa ms exp exp2 occ ind union fem blk ed, endog(exp exp2 occ ind union ed) constant(fem blk ed)
return list doesn't have anything in r(table), but ereturn list will show you that you have access to the coefficients through e(b) and the variance-covariance matrix through e(V).
You can assign these to their own matrices as follows:
matrix betas = e(b)
matrix varcovar = e(V)
Then you can use matrix commands (see help matrix) to manipulate these matrices.
As you discovered, ereturn display creates r(table) which appears quite convenient for your use. It's worth taking a look at help return for more information about the differences between the contents of return list and ereturn list.
I have a fairly complex look of code where I am looking through multiple control variables.
I am getting an error 'Invalid 'for' loop control variable
the line in questions is
for w(1) = 32 to 127
I am more familiar with VBA where I would have zero problem with this statement.
I'm guessing it has something to do with the fact that i will be looping through w(1),w(2),w(3) etc. in the same tree. I initialize the variable as dim x(10) but have also tried dim w() , dim w() redim w(10)
Any thoughts? its a fairly critical aspect of the script; as such I am unwilling to swap out all my w 1,2... for individual variables
Thoughts?
EDIT:
As per comments I should clarify a Few things:
Essentially there is a alpha numeric association with an ID in a system that I am working with which I was not handed down the key too. So I have a multi-dimensional array of rates that are used for multiplying out costs.
What I am doing is working backwards through invoices and matching a material with very subtle differences that have different pricings.
For simplicity sake, say theres a 2 dimensional material where AA, AB, ... A9 are all priced through several multiplication factors in what would just be a 2x2 grid. So maintaining a pivot point based on the position in string is very important. For this code you could take tier to mean how many characters in the string (aka how complex the composition of the material):
dim x(), w()
for tier = 1 to 2
for w(1) = 32 to 127
x(1)= chr(w(1))
If tier = 2 then
for w(2)= 32 to 127
X(2)=chr(w(2))
next
end if
str = ""
for y = 1 to (tier)
str = trim(str & x(y))
next
'''msgbox str 'debug
next
end if
str = ""
for y = 1 to (tier)
str = trim(str & x(y))
next
'' msgbox str ' debug
next 'tier
This is just an excerpt i pulled to get a basic idea of the structure w/o any calculations. this is in essence what is not working
The error is quite clear, you cannot use an Array as the control variable. The definition in For...Next Statement is even clearer;
Numeric variable used as a loop counter. The variable cannot be an array element or an element of a user-defined type.
This is one of the key differences between VBA and VBScript.
You won't loop through x(1),x(2)...on what you write it's going like this 32(1),33(1)....what type it's your w(1) and how you define him?
The SciTE editor comes with embedded Lua scripting engine having access to the text buffer of the editor. This makes it possible to extend SciTE's functionality with tools programmed in Lua and started from the Tools Menu. One such tool available from here:
http://lua-users.org/wiki/SciteSortSelection
is a tool for sorting of selected lines in alphabetical order.
Annoying for me was/is that it doesn't sort lines containing numbers in their numerical order but like this:
1
111
2
222
3
333
where I would rather expect:
1
2
3
111
222
333
Google and Co. are not of much help here as there is to my knowledge no solution to this problem available yet online. It is also not that easy to find and deeply understand the Lua documentation for table.sort(). So the question for a knowledgeable Lua programmer would be, what is the best way to patch the existing Lua script code, so that numbers (and also lines with text in case of leading spaces) become sorted as expected and the Lua code for this task runs so fast, that even sorting of huge files (50 MByte and more) won't take much time?
Your expectation is wrong. You said the algorithm is supposed to sort the texts alphabetically and that is exactly what it does.
For Lua "11" is smaller than "2".
I think you would agree that "aa" should come befor "b" which is pretty much the same thing.
If you want to change how texts are sorted you have to provide your own function.
The Lua reference manual says:
table.sort (list [, comp])
Sorts list elements in a given order, in-place, from list[1] to
list[#list]. If comp is given, then it must be a function that
receives two list elements and returns true when the first element
must come before the second in the final order (so that, after the
sort, i < j implies not comp(list[j],list[i])). If comp is not given,
then the standard Lua operator < is used instead.
Note that the comp function must define a strict partial order over
the elements in the list; that is, it must be asymmetric and
transitive. Otherwise, no valid sort may be possible.
The sort algorithm is not stable: elements considered equal by the
given order may have their relative positions changed by the sort.
So you are free to implement your own comp function to change the sorting.
By default table.sort(list) sort list in ascending order.
To make it sort in descending order you call:
table.sort(list, function(a,b) return a > b end)
If you want to treat numbers differently you can do something like this:
t = {"111", "11", "3", "2", "a", "b"}
local function myCompare(a,b)
local a_number = tonumber(a)
local b_number = tonumber(b)
if a_number and b_number then
return a_number < b_number
end
end
table.sort(t, myCompare)
for i,v in ipairs(t) do
print(v)
end
which would give you the output
2
3
11
111
a
b
Of course this is just a quick and simple example. A nicer implementation is up to you.
Below what I finally came up with myself. It's sure a quick and dirty solution which slows the already slow
( compared to jEdit [Plugins]->[Text Tools]->[Sort Lines] or to bash command line 'sort -g' )
process of sorting huge buffers of text lines, but it is at least there for use and works as expected. For the sake of completeness here the entire section of code currently present in my Lua Startup Script for SciTE:
-- =============================================================================
-- Sort Selected Lines (available in MENU -> Tools):
-- -----------------------------------------------------------
-- Specify in .SciTEUser.properties:
-- command.name.2.*=# Sort Selected Lines '
-- command.subsystem.2.*=3
-- command.mode.2.*=savebefore:no
-- command.2.*=SortSelectedLines
-- # command.shortcut.2.*=Ctrl+2 # Ctrl+2 is DEFAULT for command.2.*
function lines(str)
local t = {}
local i, lstr = 1, #str
while i <= lstr do
local x, y = string.find(str, "\r?\n", i)
if x then t[#t + 1] = string.sub(str, i, x - 1)
else break
end
i = y + 1
end
if i <= lstr then t[#t + 1] = string.sub(str, i) end
return t
end
-- It was an annoying for me that using table.sort(buffer) in Lua
-- didn't sort numbers with leading spaces in their numerical order.
-- Using following comparison function helps to avoid that problem:
function compare(a,b)
return a:gsub(" ", "0") < b:gsub(" ", "0")
-- If 'compare' is not used ( table.sort(buf) )
-- Lua uses implicit for sorting (see Lua tutorial):
-- return a < b
-- so changing the provided return statement to this above
-- would be enough to restore sorting to how it was before
end
function SortSelectedLines()
local sel = editor:GetSelText()
if #sel == 0 then return end
local eol = string.match(sel, "\n$")
local buf = lines(sel)
table.sort(buf, compare)
--table.foreach (buf, print) --used for debugging
local out = table.concat(buf, "\n")
if eol then out = out.."\n" end
editor:ReplaceSel(out)
end
-- ---------
-- :Sort Selected Lines
-- -----------------------------------------------------------------------------
I have a number of files (having 10 columns each) with following order:
file_001.txt, file_002.txt, file_003_txt,
file_021.txt, file_023.txt, file_023.txt,
file_041.txt, file_042.txt, file_043.txt,
file_061.txt, file_062.txt, file_063.txt,
file_081.txt, file_082.txt, file_083.txt,
I would like to plot each file with different line. e.g. using 1:2, using 1:3, using 1:5, using 1:8. I can not able to make a loop to call different columns. My following script is not working for k field
plot for [k=2, 3, 5, 8] for [j=0:8:2] for [i=1:3] 'file_0'.j.i.'.txt' u 1:k;
Use for [k in "2 3 5 8"] if you have a list rather than a range.
If j can be > 9, you should set up a function
fname(j,i) = sprintf("name%02.f%.f",j,i)
to get proper file names.
Format string "%02.f" means float (f), no digits after the comma (.), minimum two postions (2), fill empty space with zeroes.
print fname(2,3)
name023
print fname(13,3)
name133
print fname(113,3)
name1133
These are libc format strings, they are not documented inside the gnuplot docs, but there are many sources in the web.
I have more of a 'problem solving' question than a syntax related problem.
Briefly, I'm creating a program that will read a text file full of words (that may feasibly be a list of passwords), one word per line - I'll be using ReadLn for that bit in a loop. For every word it finds, I want it to add "an amount" of obfuscation in line with how users these days will use '3' instead of 'E' in their passwords, or '1' instead of 'I'. I work in the IT security field and password breaking is often part of it and that's what the program is for.
I have managed to create the program so far that it generates a LEET table full of many different values for each letter of the alphabet and stacks them in a StringGrid that I can access as part of the process (and it is also outputted visually to a table).
type
TLetters = 'A'..'Z';
TLeet = array[TLetters] of TStringList;
var
SourceFileName, str : string;
StartIndexFile : TextFile;
i : TLetters;
leet : TLeet;
s : string;
n, o, ColumnSize : integer;
begin
for i in TLetters do
leet[ i ] := TStringList.Create;
// The next sequence of loops populates the string grid by counting the number of characters for each letter of the alphabet and then inserting them down, column by column and row by row...
//Letter A:
s := '4 # /-\ /\ ^ aye ∂ ci λ Z';
ColumnSize := wordcount(s,[' ']);
o := 0;
for n := 0 to ColumnSize do
leet['A'].Add(ExtractWord(n,s,[' ']));
for o := 0 to ColumnSize do
StringGrid1.Cells[1,o] := Leet['A'][o];
// And so on for B - Z
// ... then an OpenDialog that opens the source text file to read. Got that sorted
// A load of file opening stuff and then the obsfucation
repeat
Readln(StartIndexFile, Str);
LblProgress.Caption := ('Parsing Index File...please wait');
OBSFUCATE THE WORDS HERE TO SOME EXTENT
// but now I have hit a barrier....
until(EOF(StartIndexFile));
My problem is this : given the word 'Edward', for example, how do I decide to what level I should obfuscate it? Just the first letter 'E' to be replaced with a '3', and nothing more perhaps? Or the first two letters 'E' and 'd' to be replaced with ALL the values in the LEET table for both of the letters E and d (meaning dozens of new words would be generated from 'Edward', and so on), or all the values for 'E' but nothing else...the list goes on. Potentially, for every word, I could create thousands of additional one's! A 100Gb source file would soon become terabytes!
In other words, I need to set "a level" for which the program will function, that the user can decide. But I'm not sure how to structure that level?
So I'm not sure how to make it work? I didn't really think it through enough before I started. My initial thoughts were "It would be cool to have a program that would take an index of words from a computer, and then generate variations of every word to account for people who obfuscate characters." but having come to code it, I've realised it's a bigger job than I thought and I am now stuck at the section for actually 'LEETing my input file'!
You could use a level (0-10) as input.
0: replace nothing
10: replace all letters with LEET letters.
Depending on the length of the word, you calculate how many letters to replace and just replace random letters in the word, so that you not always replace the first letter for level 1 etc.