copycat | simple script to capture and bin the read coverage | Genomics library

 by   MariaNattestad Shell Version: Current License: No License

kandi X-RAY | copycat Summary

kandi X-RAY | copycat Summary

copycat is a Shell library typically used in Artificial Intelligence, Genomics applications. copycat has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV). Usage: copycat alignments.sorted.bam genome_file output_prefix.
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              copycat has a low active ecosystem.
              It has 8 star(s) with 5 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              copycat has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of copycat is current.

            kandi-Quality Quality

              copycat has no bugs reported.

            kandi-Security Security

              copycat has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              copycat does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              copycat releases are not available. You will need to build from source code and install.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of copycat
            Get all kandi verified functions for this library.

            copycat Key Features

            No Key Features are available at this moment for copycat.

            copycat Examples and Code Snippets

            No Code Snippets are available at this moment for copycat.

            Community Discussions

            QUESTION

            Powershell + csv: read column 1, modify Content and write it down in column 2
            Asked 2021-May-04 at 15:25

            I'm really not that good in Powershell and only get along with a lot of Google research.

            I have a CSV File and in column 1 are a bunch of words.

            For Example:

            ...

            ANSWER

            Answered 2021-May-04 at 15:25

            If your input csv (the one with just one column) has a header above the values, read it with

            Source https://stackoverflow.com/questions/67387082

            QUESTION

            list processing in Prolog
            Asked 2021-Mar-10 at 09:17

            I am new to prolog and I'm having trouble with this problem. I am taking a sentence as input and put [Anne,do,you,know] in front of the sentence and replace any occurrence of you to I.

            For example copycat([you,love,me], X) will return X = [Anne,do,you,know,i,love,you].

            ...

            ANSWER

            Answered 2021-Mar-10 at 09:17

            First of all, you need to break this in two parts, since you want to replace every suitable element of the list by something, but you only want to add [Anne, do,you,know] once.

            So you could define your predicate like this:

            Source https://stackoverflow.com/questions/66561076

            QUESTION

            how to call the thread from a different function pyqt5
            Asked 2021-Mar-08 at 11:33
            import sys
            from PyQt5 import QtCore
            from PyQt5 import QtWidgets
            from PyQt5.QtWidgets import QMainWindow, QApplication,  QPlainTextEdit, QApplication, QMainWindow, QLabel, QComboBox
            from PyQt5.QtGui import QPixmap
            from pynput import keyboard
            from pynput.keyboard import Listener, Controller
            import pyperclip as pc 
            
            keyboard = Controller()
            class App(QMainWindow):
                def __init__(self, parent=None):
                    super(App, self).__init__(parent)
                    #super().__init__()
                    label = QLabel(self)
                    pixmap = QPixmap('E:/copycat/new.png')
                    label.setPixmap(pixmap)
                    label.setGeometry(0,0,900,400) 
                    self.title = 'COPYCAT'
                    self.left = 10
                    self.top = 10
                    self.width = 400
                    self.height = 140
                    self.initUI()
                    self.key()
            
                def initUI(self):
                    self.setWindowTitle(self.title)
                    self.setGeometry(self.left, self.top, self.width, self.height)
                    ###########
                    combo = QComboBox(self)
                    shotcut_list = ["Key.f9","Key.f2","Key.f3","Key.f4","Key.f5","Key.f6","Key.f7","Key.f8","Key.f1","Key.f10","Key.f11","Key.f12"]
                    combo.addItems(shotcut_list)
                    global shortcut
                    global cptext
                    shortcut = combo.currentText()
                    combo.setGeometry(350, 120, 120, 30)
                    combo.activated[str].connect(self.onChanged)  
                    # Create textbox
                    self.textbox = QPlainTextEdit(self)
                    self.textbox.move(20, 160)
                    self.textbox.setReadOnly(True)
                    self.textbox.resize(500,205)
                    self.setGeometry(70,70,540,388)
                    self.show()
            
                def onChanged(self, text):
                    global shortcut
                    shortcut=text
                    
                def print_key(self,key):
                    if str(key) == shortcut:
                        cptext = pc.paste() 
                        keyboard.type(cptext)
                        self.textbox.insertPlainText(cptext)
                        self.textbox.insertPlainText("\n")
            
                def key(self):    
                    listener = Listener(on_press=self.print_key)
                    listener.start()
                
            if __name__ == '__main__':
                app = QtWidgets.QApplication(sys.argv)
                ex = App()
                #ex.key()
                sys.exit(app.exec_())
            
            ...

            ANSWER

            Answered 2021-Mar-08 at 11:33

            The callback associated with on_press is executed in a secondary thread so your implementation is updating the GUI from a secondary thread which Qt prohibits, instead you should use the signals as they are thread-safe.

            Source https://stackoverflow.com/questions/66528559

            QUESTION

            How can I fix the middle column not having padding?
            Asked 2020-Dec-13 at 00:53

            I am making a copycat Drudge Report website for practice.

            While coding, I noticed that the padding doesn’t seem to work on the middle column. There’s no spaces next to the

            / separation lines, which really messes with the overall look.

            ...

            ANSWER

            Answered 2020-Dec-13 at 00:53

            It looks like HTML/CSS above is using float CSS property to achieve 3-column layout.

            This is old and inefficient way (Flexbox is preferred for columns, Grid for more complex layouts).

            The caveat with using float is that middle-column should not have width set to it and should have margin-left and margin-right which match left and right column sizes. Here's an example.

            Source https://stackoverflow.com/questions/65271179

            QUESTION

            Unchecked conversion warning with generic type in IntelliJ
            Asked 2020-Dec-02 at 15:34

            My IDE (IntelliJ) warns me about an unchecked conversion:

            Unchecked overriding: return type requires unchecked conversion. Found 'com.company.Main.Cat', required 'T'

            Nevertheless my code works as expected. Is there something I can do to prevent this warning or does my code have a "design" flaw?

            The following MCVE reproduces the warning in public Cat copy() for Cat.

            ...

            ANSWER

            Answered 2020-Dec-02 at 14:27

            Your Animal.copy method is generic, suggesting that the caller can specify the type of animal they want... but your implementation isn't generic.

            So for example, here's a slightly augmented and changed version of your code - note the change to the main method, which uses just Animal as the variable type, but specifies a type argument for the copy method:

            Source https://stackoverflow.com/questions/65109844

            QUESTION

            Duplicate fields in a form upon selection
            Asked 2020-Oct-28 at 14:12

            I made a form to select skills. After the 1st selection is made, a 2nd list is shown with options depending of the 1st choice. Then, a "+" button allow to duplicate the fields ans add another skill.

            My problem :

            The inital form is OK but when I press "+" the second form created doesn't work (the second "select field" is not filtered according to the first select.

            Please can you help?

            Thanks a lot.

            ...

            ANSWER

            Answered 2020-Oct-28 at 14:12

            You cannot use same ids for different elements so instead of id i have change that to html attributes i.e :data-id .Then , when you select any option from select-box only divs which are inside form should change not others which are added dynamically so use $(this).closest("form").. to make change inside form htmls . Lastly ,these elements are created dynamically so use $(document).on('change', 'select[name="tpl"]',...

            Also, your copycat function is copying entire div so next time if you press + it will show 2 copy of select and so on .To fix this use $('.copycat form:first')....

            Demo Code :

            Source https://stackoverflow.com/questions/64574117

            QUESTION

            Is there a way to make this code 'normal'
            Asked 2020-Aug-20 at 03:55

            i was decoding/deencrypting this code, and the python came looking like This

            ...

            ANSWER

            Answered 2020-Aug-20 at 03:55

            This is not a complete answer, but most of your file seems to look correct when it is un-escaped and printed out. For example, simply copy-pasting from your decoded.txt file into a python REPL and printing it out produces:

            Source https://stackoverflow.com/questions/63497831

            QUESTION

            fixing tabulation in c programming
            Asked 2020-Jul-09 at 16:15

            I have a file that contains id, year, name of movies, like this:

            ...

            ANSWER

            Answered 2020-Jul-09 at 10:49

            No you can never approach that kind of pretty formatting using tabs merely.

            Sticking to printf, you could use %*s format that specifies space occupation. It requires an extra number argument before the string. A positive number means right-aligned, and negative number means left-aligned. For example:

            Source https://stackoverflow.com/questions/62812996

            QUESTION

            Can I declare a delegate in an Object's New() constructor? Or with initialization parameters?
            Asked 2020-Jun-02 at 14:28

            I'm trying to declare a delegate inline with my data in C# and that doesn't seem to compile. I'm hoping someone can help me (re)structure either my thoughts or my code.

            My goal is to create different player types in an online game. Each player type has a strategy they employ. This strategy is employed by calling an inline async function that might call a HTTP REST resource as part of the IQueryable evaluation.

            Question:

            • What is a maintainable way to configure the code required within the EvaluateTurn() delegate for each of the AIPlayer types?

            More player types will be added, and the IQueryable to be a deferred execution Linq Query against CosmosDB, AzureTable, SQL, in-memory array etc.

            ...

            ANSWER

            Answered 2020-Jun-02 at 14:28

            A delegate is a type, you need to declare a property of that type:

            Source https://stackoverflow.com/questions/62154074

            QUESTION

            Discord.js Error: addRole is not a function
            Asked 2020-May-29 at 05:11

            I am having a really strange error where when I go to run my Discord Bot the console outputs the Error of yeet.addRole(Punished) is not a function. I cant understand why because I have used addRole() at the beggining of my code and that one seems to work. Can anybody tell me why this is happening??? The error occurs 9 lines from the bottom.

            ...

            ANSWER

            Answered 2018-Jan-24 at 14:04

            You're retrieving the user mention with let yeet = message.mentions.users.first();, you have to retrieve the guild member object in order to call addRole();

            So all you have to is simply change:

            let yeet = message.mentions.users.first();

            to

            let yeet = message.mentions.members.first();

            Source https://stackoverflow.com/questions/48421353

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install copycat

            You can download it from GitHub.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            CLONE
          • HTTPS

            https://github.com/MariaNattestad/copycat.git

          • CLI

            gh repo clone MariaNattestad/copycat

          • sshUrl

            git@github.com:MariaNattestad/copycat.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link

            Explore Related Topics

            Consider Popular Genomics Libraries

            Try Top Libraries by MariaNattestad

            Ribbon

            by MariaNattestadJavaScript

            Assemblytics

            by MariaNattestadJavaScript

            SplitThreader

            by MariaNattestadJavaScript

            R_for_biologists

            by MariaNattestadR

            BioCoding_Tutorial

            by MariaNattestadPython