straw | Extract data quickly from Juicebox via straw | Data Manipulation library

 by   aidenlab C++ Version: v0.0.8 License: MIT

kandi X-RAY | straw Summary

kandi X-RAY | straw Summary

straw is a C++ library typically used in Utilities, Data Manipulation, Numpy, Pandas applications. straw has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Straw is a fast implementation of reading/dump for .hic files. Available in C++, R, and Python. There are two Python versions - a pure Python one and a version where the C++ code is bound with pybind11. The latter is much faster. A Jupyter notebook example can be found here:
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              straw has a low active ecosystem.
              It has 45 star(s) with 35 fork(s). There are 11 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 25 open issues and 32 have been closed. On average issues are closed in 74 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of straw is v0.0.8

            kandi-Quality Quality

              straw has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              straw is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              straw releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

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            straw Key Features

            No Key Features are available at this moment for straw.

            straw Examples and Code Snippets

            No Code Snippets are available at this moment for straw.

            Community Discussions

            QUESTION

            2 foreach in 1 table is not work correctly
            Asked 2021-May-28 at 04:15

            I'm try to loop 2 query inside one table . both query had 10 records . so i put my first foreach (or looping) before TR tag ..

            here is example of the table that i want to create :

            ...

            ANSWER

            Answered 2021-May-28 at 04:15

            Yep, your logic is missing something because the second loop is running within the first loop, so you're creating a lot of TDs within the same TR.

            In order to achieve what you want, I suggest merging the two arrays, then looping a single array.

            Source https://stackoverflow.com/questions/67732455

            QUESTION

            Flask_SQLAlchemy, db.create_all() is unable to "see" my tables when imported though a service class
            Asked 2021-Apr-25 at 15:35

            The intent: Refactor my code into MVC (this is just the model/database part), and have the server create the database with tables on first run if the database or tables does not exist. This works when using a "flat" file with all the classes and functions defined in that file, but after moving out the functions into a service class and the models into their own folder with model classes, the db.create_all() function does not seem to be able to detect the table class correctly any more.

            Example structure, (minimum viable problem):

            server.py

            ...

            ANSWER

            Answered 2021-Apr-25 at 15:35

            The problem is that server.py is executed twice

            • when it's imported in models/users.py
            • when server.py is called to run the app

            Each execution generates a new db instance. The db imported by the model file adds the models to its metadata, the db created when the app is run has empty metadata.

            You can confirm this by printing id(db) and db.metadata.tables at the end of models/users.py and just before the call to db.create_all() in the main function.

            You need to structure your code so that only one db gets created. For example, you could move the app configuration and creation code into its own module, mkapp.py (feel free to come up with a better name):

            mkapp.py

            Source https://stackoverflow.com/questions/67254256

            QUESTION

            Can't multiply integer and double in Java?
            Asked 2021-Apr-21 at 00:26

            I'm trying to make a Java program where it calculates the total price of 3 differently valued items. Currently I'm trying to figure out why it won't let me multiply together a preset price and the amount inputted. Sorry for sloppy coding, I don't know Java basically at all. Here is code:

            ...

            ANSWER

            Answered 2021-Apr-21 at 00:26

            cup is a double type, so if you multiply a double with int you will always have a double value. Just change cupprice to double and everything will works fine

            change line 10 to double cupprice;

            Source https://stackoverflow.com/questions/67182721

            QUESTION

            how to train model in which labels is [5,30]?
            Asked 2021-Apr-19 at 12:19

            How to train on a dataset which has each label of shape [5,30]. For example :

            ...

            ANSWER

            Answered 2021-Apr-19 at 12:19

            If you do consider that the output needs to be in this shape (and not flattened), the easiest (and also correct solution in my opinion) is to have a multi-output network, each output having a layers.Dense(30,activation='softmax').

            You would have something like:

            Source https://stackoverflow.com/questions/67145393

            QUESTION

            Excel VBA or formula: Combining overlapping dates and finding non-overlaps for multiple unique ID's
            Asked 2021-Apr-18 at 15:45

            I have a very large spreadsheet with headers (180k+ rows) with unique ID's in A, start date in B, and end date in C. There are multiple rows per ID and the start and end dates overlap in a messy way.

            I need to find any gaps in the date ranges for each ID. I've written a few different formulas and macro's, tried and tweaked other VBA scripts I've found here and elsewhere. I've attempted a power query and power pivot grasping at straws, but if excel doesn't crash I'm not getting a usable output.

            Here is an example of the data I have:

            ID start end 100 1/1/2015 3/1/2015 100 3/1/2015 1/1/2300 100 1/1/2018 1/1/2019 096 7/1/2020 1/1/2021 182 9/17/2017 1/1/2018 182 1/1/2018 1/1/2019 607 1/1/2015 9/1/2015 607 9/1/2015 1/1/2017 607 1/1/2018 1/1/2020 607 1/1/2021 1/1/2300

            I would like to run a script that combines or consolidates these in someway to remove extra lines for the ID's that do not have any gaps in the date range, but will leave an extra row for the ID's that do:

            ID start end 100 1/1/2015 1/1/2300 096 7/1/2020 1/1/2021 182 9/17/2017 1/1/2019 607 1/1/2015 1/1/2017 607 1/1/2018 1/1/2020 607 1/1/2021 1/1/2300

            I don't need it to combine; though, for presentations sake it would be nice. Also, I would settle for something that is able to tell me which ID's have a gap in the range, even if it doesn't combine the dates or remove extra rows.

            Newish to VBA and formulas, though this is the first instance I've been unable to get a desired output. Any help or pointing out a better way to approach this would be greatly appreciated.

            I did find a script from another site that almost did the job, though because the date ranges cant all be sorted in proper order, like ID 100 in the example, it creates an extra line when it shouldn't. I'll paste that below.

            ...

            ANSWER

            Answered 2021-Apr-17 at 03:25

            Try this. Make sure that the data range is sorted by id and start date before you begin.

            Source https://stackoverflow.com/questions/67133524

            QUESTION

            Google Calendar API returning generic Bad Request
            Asked 2021-Apr-08 at 06:37

            I'm currently struggling with figuring out what's wrong with a Event insert I'm trying to accomplish in Flutter using Google Calendar V3 API. Initially I thought it's a matter of RFC3339 vs ISO8601 date formats, but I'm grasping at straws.

            Unhandled Exception: DetailedApiRequestError(status: 400, message: Bad Request) is what I'm getting from:

            ...

            ANSWER

            Answered 2021-Apr-08 at 06:37

            The issue is indeed related to the time, the Dart DateTime class does not format the time in a way Google likes (2021-04-12T08:30:00+03:00 which I've deduced from other languages' API implementations, and the source code of the package which does a .toString() of the DateTime basically). Fair mention that Dart DateTime does provide a String of ISO8601, Google wants an RFC3339 compliant date.

            The way around this is to create the EventDateTime from a JSON object, and to use a hacky Dart extension. I apologize for the naming but it's annoying.

            Source https://stackoverflow.com/questions/66976876

            QUESTION

            git svn fetch repeatedly fails for no apparent reason
            Asked 2021-Mar-18 at 10:20

            Background

            We are planning to do a one-way migration of SVN to Git in Azure DevOps so that we can keep our commit history of messages. As you might expect we did a trial run, after much hair pulling and standing on the shoulders of other colleagues who came before we came up with the list of commands that finally worked after 26 hours of processing.

            Those commands are:

            Run in Git Bash to get list of all authors from SVN in Git format:

            ...

            ANSWER

            Answered 2021-Mar-18 at 10:20

            I don't 100% know if the following is true but git svn fetch is now completing without errors or simply stopping part way through.

            I examined the SVN logs from the server and at the times the errors were occurring the SVN log was 0.5GB in size by the end of the day, the majority of which was not my Git migration. I suspect that there was some form of timeout occurring and that git frustratingly simply had a unhelpful or no error message. When the git svn fetch command worked the SVN logs were down to 70MB by the end of the day.

            Thus the moral of the story it seems is to check your SVN logs because git isn't going to tell you anything useful.

            Source https://stackoverflow.com/questions/66496273

            QUESTION

            How do I get Graph API delta changes due to permissions changes?
            Asked 2021-Mar-15 at 15:27

            I have an azure AD registered application. With delegated permissions of a user with AllSites.FullControl, I'm able to get drive/root/delta in Graph API.

            Problems I'm having making the delta calls as the delegated user are:

            • the deltas are not consistent. Sometimes I get results back after changing the permissions of a file/folder, sometimes I don't
            • Despite that I'm passing in these Prefer headers deltashowsharingchanges, deltashowremovedasdeleted, deltatraversepermissiongaps, I'm not getting back @microsoft.graph.sharedChanged in the response.

            The above issues are my primary questions.

            Grasping at straws here, but please let me know if I would have better luck with an app-only authentication. If so, how to get it set up with my existing Azure AD registered application, without access to Powershell or Windows (e.g. if I need to use a certificate instead of client_id/client_secret, as there is conflicting information about this, and only instructions on how to get it done with Powershell). I've already started to try to test this, but have not successfully found information on how to get this working in a multi-tenant use-case, wherein I'm trying to access the Sharepoint of an outside tenant from an Azure AD registered app-only authenticated application. All existing instructions I've seen thus far are not multi-tenant and grant themselves permissions in their own Azure AD portal.

            ...

            ANSWER

            Answered 2021-Mar-15 at 15:27

            It turned out that indeed, using app-only client credentials authentication was necessary to get @microsoft.graph.sharedChanged in the response, though this is not documented anywhere. In addition, deltas are being returned consistently now. Presumably, Microsoft is doing something to try to return only deltas relevant to the delegated user, although that is not enough in my opinion to explain for the lack of deltas in some cases. Nevertheless, I'm getting the response I need using app-only client credentials.

            Regarding use of certificate -- it was not necessary if accessing my own tenant where the app is registered, but if accessing a 3rd party tenant, a certificate was required instead of client_secret.

            Source https://stackoverflow.com/questions/66607967

            QUESTION

            Troposphere DynamoDB TimeToLiveSpecification
            Asked 2021-Jan-28 at 15:32

            I am trying to create a JSON Cloudformation template for a new DynamoDB table. I am trying to set the TimeToLiveSpecification but I get errors and the Troposphere documentation isn't clear.

            I have

            ...

            ANSWER

            Answered 2021-Jan-28 at 15:07

            Try this (untested) with the TimeToLiveSpecification shown here:

            Source https://stackoverflow.com/questions/65937862

            QUESTION

            How to refer to or coalesce a column which may not exist?
            Asked 2021-Jan-26 at 13:22

            I am creating views referring to system catalog views ( eg. pg_constraint ) which are to deployed to various databases with varying versions of postgresql. Later versions of system catalog views include columns that don't exist in prior versions of postgresql. I'd rather have a single version of my view that I can deploy widely instead of maintaining multiple versions so that when we (inevitably) upgrade some of our older databases, the view definition will not need to be updated ( who is going to remember to do that? )...

            It's probably not feasible and perhaps I'm grasping at straws but I don't want to give up so easily while it's still possible someone may have a solution.

            ...

            ANSWER

            Answered 2021-Jan-26 at 13:22

            Don't create a view on system catalogs, it will prevent you from upgrading with pg_upgrade.

            Use a function that either composes the query with dynamic SQL or executes different static queries based on the server version. You can then define a view using that function.

            Source https://stackoverflow.com/questions/65901998

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

            Vulnerabilities

            No vulnerabilities reported

            Install straw

            For the fastest version, you must have pybind11 installed. Clone the library and cd into the straw/ directory. Then run via import strawC and strawC.strawC.

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