tRep | Quick get the taxonomy of a genome

by MrOlm Python Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | tRep Summary

tRep is a Python library. tRep has no bugs, it has no vulnerabilities, it has build file available and it has low support. You can install using 'pip install tRep' or download it from GitHub, PyPI.

This program is a collection of tools for determining the taxonomy of a genome using a number of different tools. Its pretty unorgaized at the moment, but might develop into something at some point.

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Support

tRep has a low active ecosystem.

It has 5 star(s) with 3 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

tRep has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of tRep is current.

Quality

tRep has no bugs reported.

Security

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

License

tRep does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

tRep releases are not available. You will need to build from source code and install.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions are not available. Examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed tRep and discovered the below as its top functions. This is intended to give you an instant insight into tRep implemented functionality, and help decide if they suit your requirements.

Run Prodigal
Generate a taxonomy string from a set of hits
Generate the full TDDB for the given hits
Returns lineage name for a taxid
Generate taxonomy from TDB
Filter out the results that are less than min_diff
Load hits from Centrifuge results
Convert b6 to TDB
Extract the name of a diamond scaffold
Load b6 file
Returns the type of b6
Add BDB to TDB
Load scaffold
Given a tt_loc
Return the version number

Get all kandi verified functions for this library.

tRep Key Features

No Key Features are available at this moment for tRep.

tRep Examples and Code Snippets

No Code Snippets are available at this moment for tRep.

Community Discussions

Trending Discussions on tRep

Pandas pivot_table: Defining Columns

Debug manifest .mpd

Replace multiple occurrences between two strings

Synchronized Thread Communication is Java - Using only Primitive Constructs

How can I resolve this matter (c++ template with typedef)

QUESTION

Pandas pivot_table: Defining Columns

Asked 2020-Jan-18 at 16:32

I'm new to pandas and python in general. I'm pulling data from an Access database and creating a pivot table.

...

ANSWER

Answered 2019-Mar-13 at 03:38

I suppose you can always put some 'touch-up' onto the df once it's been created. For example, you can add a column and fill it up with nan i.e. df['C'] = np.nan

Source https://stackoverflow.com/questions/55133790

QUESTION

Debug manifest .mpd

Asked 2018-Apr-12 at 14:47

After activating CORS on my webserver I have run my manifest on dash conformance webtool finding several errors that I can not interpret, at the moment I am not able to get the ABR behavior,Can i ask for help to understand how to fix the bug?

https://allibrante.com/live/manifest.mpd

Below some log reported from the Dash confromance webtool, for more details is better run the manifest on their webtool

Thanks a lot!

error: moov-1:trak-1:mdia-1:minf-1:stbl-1:stsd-1 SampleDescription sdType must be 'mp4v', 'avc1', 'encv', 'hev1','hvc1', or 'vp09'('mp4v', 'avc1', 'encv', 'hev1','hvc1','vp09')
Warning: Unknown atom found "avcC": video sample descriptions would not normally contain this Warning: Unknown atom found "pasp": video sample descriptions would not normally contain this Brand 'lmsg' not found as a compatible brand for the last segment (number 3); violates Section 3.2.3. of Interoperability Point DASH264: If the MPD@type is equal to "dynamic" or if it includes MPD@profile attribute in-cludes "urn:mpeg:dash:profile:isoff-live:2011", then: if the Media Segment is the last Media Segment in the Representation, this Me-dia Segment shall carry the 'lmsg' compatibility brand tfdt base media decode time 1658.000000 not equal to accumulated decode time 0.000000 for track 1 for the first fragment of the movie. This software does not handle incomplete presentations. Applying correction.
error: Buffer underrun conformance error: first (and only one reported here) for sample 1 of run 1 of track fragment 1 of fragment 1 of track
id 1 (sample absolute file offset 1356, fragment absolute file offset 860, bandwidth: 7591)

'tkhd' alternateGroup must be 0 not 1 Validate_ES_Descriptor: ES_ID should be 0 not 2 in media tracks

WARNING: unknown sample table atom 'sgpd' WARNING: unknown mvex atom 'trep' WARNING: unknown/unexpected atom 'meta' Brand 'lmsg' not found as a compatible brand for the last segment (number 3); violates Section 3.2.3. of Interoperability Point DASH264: If the MPD@type is equal to "dynamic" or if it includes MPD@profile attribute in-cludes "urn:mpeg:dash:profile:isoff-live:2011", then: if the Media Segment is the last Media Segment in the Representation, this Me-dia Segment shall carry the 'lmsg' compatibility brand tfdt base media decode time 1657.984000 not equal to accumulated decode time 0.000000 for track 2 for the first fragment of the movie. This software does not handle incomplete presentations. Applying correction.
error: grouping_type roll in sbgp is not found for any sgpd in moof number 1 error: grouping_type roll in sbgp is not found for any sgpd in moof number 1 error: grouping_type roll in sbgp is not found for any sgpd in moof number 1

...

ANSWER

Answered 2018-Apr-12 at 14:47

The cause of the majority of your problems is spelled out in the error message: This software does not handle incomplete presentations. You are trying to validate a live stream, and this tool does not currently have that capability.

With respect to the sample description issue, it looks like the validator does not recognise avc3 content (ie where the parameter sets are inband rather than in the initialisation segment). I would consider this a bug and suggest you raise an issue at https://github.com/Dash-Industry-Forum/Conformance-and-reference-source/issues.

Source https://stackoverflow.com/questions/49792446

QUESTION

Replace multiple occurrences between two strings

Asked 2018-Jan-06 at 03:19

I need to replace every character a between xx and zz with hello:

...

ANSWER

Answered 2018-Jan-05 at 00:35

Your problem is with the .* as . will match every character including white space. You should use \S instead as it will match all non-white space characters:

Source https://stackoverflow.com/questions/48105521

QUESTION

Synchronized Thread Communication is Java - Using only Primitive Constructs

Asked 2017-May-31 at 00:08

I'm struggling to achieve the perfect communication between my Server and Client Thread Sub-classes (Simulation). I read many articles, But I think I'm not getting the basic concept of how to synchronize threads.

Issue:
My Server is receiving the requests from all three clients and after shutting down, Clients are printing the reply they got from server. But Server should respond a Client first and then should get another request from other threads. Your kind help will really be appreciated. Thanks

Below are the Classes which are involved:
Server.java

...

ANSWER

Answered 2017-May-31 at 00:08

I think what you want is to just put the entirety of your Server's run() method inside a loop:

Source https://stackoverflow.com/questions/44273578

QUESTION

How can I resolve this matter (c++ template with typedef)

Asked 2017-Feb-27 at 05:02

//trep.h

#include 

template 
typedef std::pair, Trep> TrepPair; //error!


template 
class Trep {

    public:
    type key;
    int priority, size;
    Trep *left, right;

    Trep(type _key) :
        key(_key), priorty(rand()), size(1), left(NULL), right(NULL) {}


    TrepPair splited(Trep &root, type key);
    Trep* insert(Trep &root, Trep &node);

};

...

ANSWER

Answered 2017-Feb-27 at 04:24

There's no such thing as "template typedef" in C++.

Instead, C++11 introduced template using.

Source https://stackoverflow.com/questions/42477805

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

Vulnerabilities

No vulnerabilities reported

Install tRep

You can install using 'pip install tRep' or download it from GitHub, PyPI.
You can use tRep like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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 .

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