puzzle | Variant caller GUI genetic disease analysis | Genomics library
kandi X-RAY | puzzle Summary
kandi X-RAY | puzzle Summary
Note to users and collaborators: We developed Puzzle as an alternative to Scout which would be easy to install and use for anyone. We have since worked a lot with these aspects on the former software and decided to focus our efforts there. Scout features the same SNV and SV views and we are continuing to add features - please check it out: Variant Caller GUI and genetic disease analysis tool.
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Top functions reviewed by kandi - BETA
- View variants
- Bind extensions to app
- Create a Flask application
- Configure Flask app
- Add transcripts to a variant
- Adds a transcript to this variant
- Construct a SnpEff transcript object
- Show all variants for a case
- Parse the filters
- Adds a suspect
- Read the long description from the README file
- Bootstrap the command line interface
- Delete a suspect from the database
- Delete a comment from the database
- Create the database
- Add the thousand_g
- Upload an individual resource
- Add gene information to a variant object
- Add GMAF to a variant
- Recursively parse requirements file
- Add HGNC symbols to a variant
- Add ExAC frequency
- Configure the root logger
- Get gene information for a variant
- Load a variant source
- Delete a resource
puzzle Key Features
puzzle Examples and Code Snippets
Lines of Code : 12License : Strong Copyleft (CC BY-SA 4.0)
Copycounter = 0
items = [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 ,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]
from itertools import permutations
for A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z in per>>> f = open("test.png", "rb")
>>> header = f.read(8)
>>> header
b'\x89PNG\r\n\x1a\n'
>>> header.hex(" ", 1)
'89 50 4e 47 0d 0a 1a 0a'
# Uses pseudo-namespacing to avoid collisions.
_EXT_SUFFIX = "___"
_NEXT_EXT_INDEX = 0
def is_ext_var(element) -> bool:
return element.endswith(_EXT_SUFFIX)
def ext_var() -> str:
global _NEXT_EXT_INDEX
ext_index = _NEfrom rich.panel import Panel
from rich.text import Text
from textual.app import App
from textual.widgets import Header, Footer, ScrollView
class MyApp(App):
async def on_load(self) -> None:
await self.bind("b", "color('bldf.groupby(['ProdName','Year'])['OrderID'].count()
ProdName Year
Puzzle 2015 1
2016 1
Toy Car 2015 2
2016 2
Train Set 2015 1
2016 1
Name: OrderID, dtype: int64
session.add(puzzle)
db.session.query(Category.name).filter_by(name=cat).first()
db.session.query(Category).filter_by(name=cat).first()
In [1]: import random
In [2]: [random.sample(range(1, 10), 9) for _ in range(9)]
Out[2]:
[[3, 9, 8, 1, 2, 5, 6, 4, 7],
[6, 7, 3, 9, 2, 5, 8, 1, 4],
[4, 1, 9, 2, 7, 3, 5, 6, 8],
[3, 5, 9, 4, 2, 1, 7, 8, 6],
[7, 2, 8, 6, 1, 9, 4, 5, 3],weekday = ('Mon,', 'Tue,', 'Wed,', 'Thu,', 'Fri,', 'Sat,', 'Sun,')
with open(inf, "r") as infile:
with open(outf, "w") as outfile:
# If you intend to call the .write() method, it will need an argument
# so thatinf = "/Users/dusti/Documents/datetime25.txt"
outf = "/Users/dusti/Documents/datetime30.txt"
weekday = ('Mon,', 'Tue,', 'Wed,', 'Thu,', 'Fri,', 'Sat,', 'Sun,')
with open(inf, "r") as infile:
with open(outf, "w") as outfile:
oimport os
os.system("python -m pip install -r requirements.txt")
Community Discussions
Trending Discussions on puzzle
QUESTION
There are a number of different ways, that make a type/class usable in a ranged for loop. An overview is for example given on cppreference:
range-expressionis evaluated to determine the sequence or range to iterate. Each element of the sequence, in turn, is dereferenced and is used to initialize the variable with the type and name given in range-declaration.
begin_exprandend_exprare defined as follows:
- If
range-expressionis an expression of array type, thenbegin_expris__rangeandend_expris (__range+__bound), where__boundis the number of elements in the array (if the array has unknown size or is of an incomplete type, the program is ill-formed)- If
range-expressionis an expression of a class typeCthat has both a member namedbeginand a member namedend(regardless of the type or accessibility of such member), thenbegin_expris__range.begin()andend_expris__range.end()- Otherwise,
begin_exprisbegin(__range)andend_exprisend(__range), which are found via argument-dependent lookup (non-ADL lookup is not performed).
If I want to use a ranged for loop say in a function template, I want to constrain the type to be usable in a ranged for loop, to trigger a compiler error with a nice "constraint not satisfied" message. Consider the following example:
...ANSWER
Answered 2022-Apr-14 at 09:51It seems like what you need is std::ranges::range which requires the expressions ranges::begin(t) and ranges::end(t) to be well-formed.
Where ranges::begin is defined in [range.access.begin]:
The name
ranges::begindenotes a customization point object. Given a subexpressionEwith typeT, let t be an lvalue that denotes the reified object forE. Then:
If
Eis an rvalue andenable_borrowed_range>isfalse,ranges::begin(E)is ill-formed.Otherwise, if
Tis an array type andremove_all_extents_tis an incomplete type,ranges::begin(E)is ill-formed with no diagnostic required.Otherwise, if T is an array type,
ranges::begin(E)is expression-equivalent tot + 0.Otherwise, if
auto(t.begin())is a valid expression whose type modelsinput_or_output_iterator,ranges::begin(E)is expression-equivalent toauto(t.begin()).Otherwise, if
Tis a class or enumeration type andauto(begin(t))is a valid expression whose type modelsinput_or_output_iteratorwith overload resolution performed in a context in which unqualified lookup forbeginfinds only the declarations
QUESTION
Why does this happen in Python?
float('inf') == float('inf')returnsTrue,float('inf') + float('inf') == float('inf')returnsTrue,float('inf') * float('inf') == float('inf')returnsTrue,float('inf') - float('inf') == float('inf')returnsFalse,float('inf') / float('inf') == float('inf')returnsFalse.
My best guess, if I think about limits, is related with the result of this operation:
limx→+∞(f(x) ▢ g(x)) where limx→+∞ f(x) = +∞ and limx→+∞ g(x) = +∞, which returns +∞ if ▢ is + or *, but it is not defined (it could return every value) if ▢ is - or /.
I am very puzzled, though.
...ANSWER
Answered 2022-Mar-09 at 17:54Before the comparison of
QUESTION
I am wondering how to solve this problem with basic Python (no libraries to be used): How to calculate when one's 10000 day after their birthday will be (/would be). For instance, given Monday 19/05/2008 the desired day is Friday 05/10/2035 (according to https://www.durrans.com/projects/calc/10000/index.html?dob=19%2F5%2F2008&e=mc2)
What I have done so far is the following script:
...ANSWER
Answered 2022-Mar-06 at 18:02Using base python packages only
On the basis that "no special packages" means you can only use base python packages, you can use datetime.timedelta for this type of problem:
QUESTION
I have the following instruction: mov r1, r7 in my assembly code but after looking into disassembly, I've found that actual generated code was adds r1, r7, #0
I checked with ARMv6-M Architecture Reference Manual and I found out that there's MOVS , instruction (A6.7.40) which is different from ADDS.
While that's not a big issue, I'm still puzzled why assembler replaces code that I wrote by different op-codes. According to the book that I'm reading, all non-jump instructions take 1 cycle (and I'd prefer for assembler to be dumb rather than trying to optimize something for me).
I'm using Raspberry Pi Pico SDK which uses GNU Assembler, AFAIK.
All my code is written in helloworld.S, full source code is:
...ANSWER
Answered 2022-Mar-06 at 21:36Can I suggest that you add:
QUESTION
I am attempting to solve a coding challenge however my solution is not very performant, I'm looking for advice or suggestions on how I can improve my algorithm.
The puzzle is as follows:
You are given a grid of cells that represents an orchard, each cell can be either an empty spot (0) or a fruit tree (1). A farmer wishes to know how many empty spots there are within the orchard that are within k distance from all fruit trees.
Distance is counted using taxicab geometry, for example:
...ANSWER
Answered 2021-Sep-07 at 01:11This wouldn't be easy to implement but could be sublinear for many cases, and at most linear. Consider representing the perimeter of each tree as four corners (they mark a square rotated 45 degrees). For each tree compute it's perimeter intersection with the current intersection. The difficulty comes with managing the corners of the intersection, which could include more than one point because of the diagonal alignments. Run inside the final intersection to count how many empty spots are within it.
QUESTION
here is a puzzle that I keep on bumping into and that, I believe, no previous SO question has been addressing: How can I best use the lens library to set or get values within a State monad managing a nested data structure that involves Maps when I know for a fact that certain keys are present in the maps involved?
ANSWER
Answered 2022-Feb-09 at 11:43If you are sure that the key is present then you can use fromJust to turn the Maybe User into a User:
QUESTION
I am sorry but I am really confused and leery now, so I am resorting to SO to get some clarity.
I am running Android Studio Bumblebee and saw a notification about a major new release wit the following text:
...ANSWER
Answered 2022-Feb-10 at 11:10This issue was fixed by Google (10 February 2022).
You can now update Android Studio normally.
QUESTION
An old code base I'm refactoring has a rather unorthodox way to access n dimensional vectors by overloading the () operator instead of the [] operator.
To illustrate, suppose Vec is a class that overloads both operators for indexing purpose of an internal list of doubles.
...ANSWER
Answered 2022-Feb-04 at 15:52One "problem" with [] is when you have multiple dimensions. With an array you can do arr[val1][val2], and arr[val1] will give you an array you can index with [val2]. With a class type this isn't as simple. There is no [][] operator so the [val1] needs to return an object that [val2] can be applied to. This means you need to create another type and provide all the functionality you want. With (), you can do data(val1, val2) and no intermediate object is needed.
QUESTION
I was testing this code (https://godbolt.org/z/fe6hhbeqW)...
...ANSWER
Answered 2022-Jan-29 at 13:14It doesn't matter that i is guaranteed to be evaluated only at compile-time when its value is known in an abstract sense.
It also doesn't matter whether the function is consteval or constexpr or none of these.
The language is still statically typed and nth_type_t; must in any given instantiation of the function refer to exactly one type. If i can change in the for loop, that is not possible to guarantee.
The language requires that the expression i when used as template argument is by itself a constant expression, independently of whether the whole function body can only be evaluated as part of a larger constant expression. But i is neither declared constexpr, nor declared const with constant initializer.
QUESTION
the below method compiles without problems:
...ANSWER
Answered 2021-Dec-21 at 14:14Compatibility with the return type Stream> in the first case is not obtained by virtue of numbers.map(Optional::of) returning a Stream> on its own; it's the compiler inferring the return type of numbers.map(...) due to it being a generic method:
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